I can help you with questions regarding Russia and the Ukraine. I have a few ideas regarding the area. Sorry for the wall of text in this post.
Some things about the separatists
The separatist area should be a single state, Novorossiya or New Russia. Novorossiya means New Russia in Russian, so it is up to you if you want to use the transliterated Russian name or the English translated name for the mod. NR should have claims on the entire southern and eastern provinces, and cores on the Donetsk and Lugansk Oblasts of which they currently only control half of,
here's a map, light green - claims, dark green - cores. The separatists have sympathisers in every province though, so if they get control of that territory it should become a core within 2 years. Donetsk and Lugansk republics are separate in name only, in practice they have a unified armed forces and rely on Russia for support anyway. DH mechanics would not work well with having 2 tiny states like that IMO, better to keep it as one state. And this is also the opinion of the population, they don't care about separate Donetsk or Lugansk polities, they care about forming Novorossiya, separating from Ukraine, and unifying with Russia. In that order. By the way your borders for the separatists on post #4780 are correct.
Suggestion for flags for NR:
national flag,
war flag. The "war flag" is actually much more common in public displays in Russia, Donetsk, and Lugansk than the "national flag" so you can use the war flag for both purposes in the mod if you wish.
There is an airport in Mariupol.
NR should be granting military access to Russia since game start.
NR units should all have anti-air attachments, this is actually very important as the Ukrainian Air Force was rendered essentially useless since mid-last year because of the separatist anti-air capabilities.
Also in the mod World in Flames 2, Germany gets a decision to have military control over Franco's forces in the Spanish Civil War, but they aren't actually in an alliance. If you can somehow do that for Russia and NR, Russia having military control over NR army but without being allied, that'd be the closest representation of their relationship.
Financial support for NR
Russia should be given a decision to financially support NR to varying degrees:
1) Totally subsidise (large support)
2) Partially subsidise (medium support)
3) Financial aid (small support)
This will give a steady supply of resources to NR so it doesn't just collapse.
Russo-Ukrainian War (Russian decides to invade)
Russia should have the decision to launch full-scale invasion of the Ukraine at any time, but at a high economical cost, and costly occupation afterwards (costly in economic terms, not military). Once Russia invades, you could have decisions for the EU countries on voting about sanctions on Russia. You could also give a decision for Russia to bribe one of the EU states to veto the sanctions. At the conclusion of the war, Russia should be given a decision on the fate of the Ukraine:
1) NR is expanded to all of its cores, NR gets 10% dissent lowered, Russia gets 5% dissent lowered, Ukraine gets 10% dissent, small sanctions
2) NR is expanded to all of its claims, NR gets 20% dissent, Russia gets 10% dissent lowered, Ukraine gets 30% dissent, medium sanctions
3) NR is expanded, Ukraine becomes a puppet state, Karpatalja gets independence as a Russian puppet state, Russia gets 10% dissent lowered, NR gets 20% dissent, Ukraine gets 90% dissent, very heavy sanctions
4) NR is expanded, Ukraine becomes a puppet state, Karpatalja gets independence as a Russian puppet state, Galicia gets independence, Carpathian Rus gets independence as a Russian puppet state, Russia gets 10% dissent lowered, NR gets 20% dissent, Galicia gets 20% dissent, Ukraine gets 40% dissent, heavy sanctions
Karpatalja by the way is what Hungarians call the Zakarpattia Oblast, in game the Hungarian majority-area would be the Uzhorod province in southwestern Ukraine.
Here's a map for this
Russia could have a decision to offer Hungary the unification of Karpatalja and Hungary in return for Hungary leaving NATO and becoming neutral.
And Carpathian Rus would be a pro-Russian separatist state.
For options 3-4 Ukraine should then get a name change to Malorossiya or Little Russia, again pick which name you prefer for the mod.
New Russia and Little Russia should, at the conclusion of the war, become allied to Russia and each other, giving each other military access. And Russia having military access through both.
Russia should get a boost in monetary income (small one for 1-2, medium one for 4, and large one for 3) because it will no longer have to pay tariffs for the use of the
gas pipelines running through the Ukraine, and will actually gain physical control over them. Russia should also get events about Ukrainian nationalist partisans attacking the pipelines in this scenario.
Russo-Ukrainian War (Ukraine decides to invade the separatists)
Ukraine should have a decision to invade NR any time, but if it chooses to do so, Russia should get a decision about intervention:
1) Aid NR with overt military action
2) Aid NR with covert military action
3) Abandon the NR
For option 1, Russia would declare war on Ukraine and everything else continues as up above.
For option 2, NR would be given some military units, Russia donates some supplies, and some manpower is subtracted from Russia and given to NR.
For option 3, NR stops being a puppet of Russia, the NR relinquishes military access and control for Russia, and their trade cancelled.
Ukraine shuts down Russian gas pipelines
For peacetime prior to war, you could also add a decision for Ukraine to shut down the pipelines (this will give a monetary penalty to Ukraine and a larger one to Russia, but decreases dissent by 7% for Ukraine), but this will trigger a decision for Russia:
1) Threaten Ukraine with war if it shuts down the pipelines
2) Do nothing, get 8% dissent
If Russia does threaten war, Ukraine should have the decision to:
1) Back down, get 5% dissent
2) Do not back down
If Ukraine backs down, Russia should have its dissent lowered by 2%
If Ukraine doesn't back down, Russia should have the decision to:
1) Declare war on Ukraine
2) Back down, get 5% dissent
If Russia backs down, Ukraine should have its dissent lowered by 10%
Moldova and Transnistria
Transnistria as well I think should be represented as a Russian puppet, with Russia having military access and military control over Transnistria in game. There is also a small 1,200 unit of the Russian army stationed in Transnistria, so you could represent that somehow. Russia could have a decision to get Transnistria to join the war against Ukraine. Meanwhile Moldova could take the opportunity of Russia's distraction in Ukraine by attacking Transnistria and bringing it back under Moldovan control. Russia should have the option to intervene against Moldova and liberate Transnistria if it is occupied by the time Russia re-enters the area. Russia should also have the option to liberate a "Republic of Gagauzia and Taraclia" (this is something I made up) in the province of Comrat on the map, and it would be a Russian puppet. A Gagauzia separatist republic did exist during the War of Transnistria, but it accepted to have autonomy instead of independence like Transnistria.
Gagauzia is populated by Gagauzians (a Turkic people), while
Taraclia is populated by Bulgarians.
Russia could then have a decision to offer Moldova to Romania in return for Romania leaving NATO and becoming neutral.
Belarus becomes a puppet
After the end of the war in the Ukraine, Russia should have a decision to approach Belarus about it becoming a puppet in return for a favourable trade agreement. Belarus would then have the option to:
1) Refuse and break away from Russia's sphere
2) Refuse but remain in Russia's sphere
3) Accept the Russian proposal
For option 1, Russia should have the decision to threaten Belarus with war if it refuses Russia's proposal. Belarus would then have the option to back down and accept Russia's proposal or still break away. If it chooses the latter, Belarus would break its alliance with Russia and relinquish military access for Russia. It would then announce its intention to join the EU and NATO. Belarus would also change its flag to the
nationalist white-red-white tricolour to symbolise it breaking away from Russia. Russia would then have the option to invade Belarus and make it a puppet, or accept it breaking away and Russia gains 15% dissent.
For option 2, Russia here should also have the decision to threaten Belarus with war if it refuses. And then same as option 2, it can accept or break away from Russia's sphere and so on.
For option 3, Belarus should change its name to Byelorussia or White Russia. Again, go with the name you feel is better for the mod: the Russian transliteration into English, or the English translation.
Eurasian Union
The way I understand it, is Kazakhstan was reluctant to enter a political union with Russia without Ukraine there as well as a way to balance out the Russian economy. IRL Kazakhstan got it lessened to an economic union rather than a political one. Now that in this scenario of Russian victory, Ukraine will most certainly join it, I think Kazakhstan in this case would feel more pressure to join a Russian-led Eurasian Union. The other members of the Eurasian Economic Union (IRL) are more reliant on Russia, like Armenia and Kyrgyzstan and would join without a fuss. Tajikistan is the most likely addition. So the way this will work in game is Russia gets a decision to establish a political union with its allies New Russia, Little Russia, White Russia, Armenia, Kyrgyzstan, and Kazakhstan. Seeing as how South Ossetia, Abkhazia, Transnistria, and Nagorno-Karabakh are in frozen conflicts, they wouldn't be official members however there should be some options to change that. If Moldova was annexed by Romania, then the frozen conflict does not exist anymore between Transnistria and Moldova, so it would be free to join the Eurasian Union. Armenia, Kyrgyzstan, and Kazakhstan should not be puppets of Russia, but members of the Eurasian Union should get a small increase to industrial efficiency or some other economic gain. Later there could be decisions for
Russia to centralise the Eurasian Union, and Russia would annex the other members.
Russian separatists in the Baltic states
Now, this is the one that could be really interesting in the mod, potentially sparking WW3. It'd go something like "Inspired by the success of Russian separatists in the Ukraine and the expansion of the Russian world to White Russia and Little Russia, and angry at their status as second class citizens in the Baltic states, Russians in Estonia and Latvia begin forming militias and stage referendums in their regions on declaring independence and joining Russia".
Map of ethnic Russians in the Baltic states
The separatist states would be called the Narva People's Republic and the Dvinsk People's Republic. On the
E3 map they would be in the provinces of Narva, Estonia and Daugavpils, Latvia respectively. Dvinsk by the way was the name of Daugavpils from 1893-1920, since then it has been known as Daugavpils. As they declare independence, NPR should be at war with Estonia, and DPR should be at war with Latvia. Russia should then get the decision to intervene:
1) Intervene overtly
2) Intervene covertly
3) Abandon the separatists
For option 1, Russia would invade Estonia and Latvia, and another rebellion would occur in Lithuania, this time by Polish separatists in Wilno/Vilnius, who see the Russian intervention as their best chance for separation from Lithuania. They then declare independence as the Wilno People's Republic. I didn't make this up by the way, there is a
Polish facebook page dedicated to such a scenario haha. Russia could then choose to support the separatist Poles or not.
For option 2, the NPR and DPR would receive some military units, Russia would donate some supplies, some manpower would be subtracted from Russia and given to the NPR and DPR Russia would also get them as puppets, gain military access, and military control over them.
For option 3, Russia does nothing, at the cost of gaining 12% dissent.
If options 2-3 happen, then some decisions could be made for NATO as a whole to either intervene directly, intervene indirectly, or sit back. Intervening indirectly will mean just the Baltics get some military units, supplies, and manpower but NATO won't go to war. If NATO chooses to intervene directly then if Russia chose option 1, it'd be cool to see some kind of limited war between NATO and Russia for control of the Baltic states, but I don't know if it's possible to have the AI fight only in a certain area while ignoring other areas in DH, so I don't know. If limited isn't possible, then this is full-scale war between Russia and NATO. If Russia had chosen option 2, then NATO could decide to invade the separatists, which will trigger a decision for Russia to go to war with NATO or let them beat the separatists in the Baltics.
Now should Russia gain control of the three Baltic states one way or another, it should get a decision to create to replace the three Baltic states with a single "Baltic Federation" and have it as a puppet state. I don't know what you should call this entity maybe "Pribaltika" as the name would be in Russian, but if you call it that then you should call Transnistria by its Russian name too then: "Pridnestrovie". I'm in favour of the Russian names by the way

The Wilno People's Republic would remain independent as a Russian puppet but there could be a decision for Russia to offer Poland a unification with the WPR in return for Poland leaving NATO and becoming neutral.
I can do some flags and ministers but I'm not sure if I could finish the latter because a lot of what I came up with hasn't happened. Flags should be pretty easy to find, or make them myself in FlagMaker. Let me know what you think Nova