-What are the S % and M % figures next to generals' names?
S is for supplies, M is more Morale
-How to transfer deeds?
Move generals into the same settlement, ship or army and drag and drop onto the other generals pic
-How to transfer the supply wagon?
same as above
-Which conditions must be met before erecting a building so that I don't get the "Manpower deficit" debuff?
buildings have nothing to do with manpower deficit. Just if you go into deficit you will not be able to build new buildings or raise taxes so if you must recruit more men than you have available first queue up all the buildings you want and set the tax rate.
-What is "Manpower deficit" and how does it affect my gameplay/stats/whatever really?
Is when you train more men than are readily available for training(you set in January every year) As to game play it only effects the settlement that you went into deficit as mentioned above you won't be able to recruit or build anything until you get back into positive manpower. Either by disbanding units in that settlement or in January the next year.
-Does the mod have to be played on VH/VH to work properly? Are the AIs just bluntly buffed with increased income and unit stats the higher the difficulty level?
BYG wrote BGRV as a part of VH/VH and he himself does not know to my knowledge what will happen if you play on something lower. As to the AI buffs there are not any really no money scripts that just throw money at the AI or anything. It is possible to bankrupt another faction is you want to and then go from there. There units do not get any buffs either.
It's always best when we can find answers for ourselves. You can try to search and see if it was asked before as well but I don't mind answering questions. If you still don't quite understand something just ask. BGRV is very detail oriented can't just hit end turn without looking into what's going on after every turn