[slightly edited your post so i can answer point to point hope you dont mind]
1.) It looks like AI is very trigger happy, specially on day one game start, mostly because nobody has 100% (or even close to) land force limit, apart from changing overall strategic situation, there is nothing i can do about it, and to be quite honest im not sure that i want to; Castille should* rise most of the time to dominate Iberia, so that later game, specially Colonial age can develop properly. On top of that, Aragon can do one sneaky thing AI in general often fails to counter - it can form alliance with Portugal (which isnt quite a push over as in vanilla), if they do Castille is almost guaranteed to lose the first war.
2.) This is not a MPM issue, its AI related in general, i think you must have been playing an older version of MPM, in last few ive added/changed stuff to make sure Ottomans swarm stuff around them. Apart from making all Turkish minors tribal, and putting them in Muslim group (Persia flavored), i also added couple of events (that are still somewhat raw need to write proper English localizations and that takes time) which should over time reduce the relations between tribal and non-tribal countries, so there is simply no way that AI Ottomans will sit there with 200 relations with Karaman/Candahar/Ramazan/Dulkadir and co (unless human plays Ottos and maintains the relations on purpose of course).
3.) Regardless of actual relations, nations who happen to own a HRE province on start date, or who happen to acquire HRE provinces, without being HRE members themselves will always attempt to remove imperial influence from these provinces, if a.) they are at peace b.) the said province is HRE and core = THIS. Having HRE provinces while not being HRE member yourself is not a very good thing (specially if youre a minor, medium or local power), think of it as having a German guy somewhere in HRE thinking he has full legal authority to meddle in your domestic affairs. Naturally you'd wanna prevent that at all costs, unless you wish to enter his sphere of influence of course.
4.) This was spotted and should have been fixed 1 or 2 versions ago, ill have to check it out, but im fairly certain they all have proper cultures now. It happened when i messed up a development version EU3 so i had to install somewhat outdated version of files, kinda forgot to fix everything at first. Will look into that.
5.) Working as designed, IIRC they should also be capable of forming Mughals fairly often too. Is it a good or bad thing? I have no idea, my guess is that its one of those things where the question of how good the outcome is for you, actually depends on where you are or whats your point of view. A Hindu minor that borders them might not be very happy about it, but a Russian minor on the other hand might feel very lucky that there is someone out there who is gonna mess with Timmies and GH thus making their lives that much easier.
6.)a) Im glad you like it
6.)b) Hmmm i like general idea, can you be a bit more specific on what kind of bonuses youd want?