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Are there any good guides for this game? I am a bit lost with all the differences from HoI3.
There is the manual right here: https://forum.paradoxplaza.com/forum/index.php?threads/darkest-hour-manual.542573/ . It might not be up to date for 1.04, but it is perfectly capable of giving you a clear understanding of the game.

Aside from that, you have a lot of wonderful AARs to choose from. I recommend this: https://forum.paradoxplaza.com/forum/index.php?threads/aarchtung-panzer-ii-wif2.688899/ because the mechanics of WiF 2 aren't that different from vanilla DH and most mods for DH, unlike say... TRP for which I am doing an AAR right now.
 
The Minister's effect " Naval Reseach Time: -10% ", does include the Naval Doctrines?
No. This bonus is applied only for naval units research.
There are separate commands for each technology group:

Code:
#     research - Gives bonus to research time and cost. 
#            which =    all (default ) / infantry / armor / naval / aircraft / industry / land_doctrines 
#                / secret_weapons / naval_doctrines / air_doctrines
#            when = time (default ) / cost
#            value = (-)x.xxxx - Negative values are bonuses, positive - penalties.

naval_doctrines is the one that alters naval doctrines research.
 
1 - In which file do I find a country's available heads of government and state?
2 - The manual states that national socialism (and apparently fascism as well) enjoys better international standing than stalinism (and leninism I presume). However I see no evidence that stalinism enjoys more social/economical slider freedom than national socialism. Does stalinism have any hidden bennefit to balance it out?
 
Thank You, I was in doubt as I haven't yet found a Minister with Doctrines research bonus.

Now that minister traits are moddable, you can add that as a bonus or create new traits with that bonus. :)
 
Are there any good guides for this game? I am a bit lost with all the differences from HoI3.

Since vanilla Hoi2 is playable with DH, I suggest you start it up, play the tutorial, then have a look at the battle scenarios. Start with the ardennes offensive one, which will learn you a bit about combat, when having played that once or twice, try the Spanish civil war one, which will learn you a bit about both production and warfare. After that you can switch to DH and try a full campaign. :)
 
Do I need full orga to conduct an amphibious landing?

my first landings in the war all worked smoothely but in the last three the fleet simply returned to the navalbase without conducting the landing. My orga was not full.

Is this different for different unit types (say marines)?
 
Do I need full orga to conduct an amphibious landing?

my first landings in the war all worked smoothely but in the last three the fleet simply returned to the navalbase without conducting the landing. My orga was not full.

Is this different for different unit types (say marines)?
It depends on the naval unit and can be set when you start each naval mission (same for air missions).