"What units are paid by wages and how much does what unit cost per turn?"
in standard M2TW games there should be only agents (and not all of them); I think it is the same in TATW.
"But how much does the different kinds of units get?"
it is reported on the sheet of each agent; IIRC spies have 200, diplomats 100, assassins ...

I think you can also see on the descr_character.txt to be sure of the costs
"Also my general units get paid over the wages? 250 per general? Is the upkeep for the bodyguard also paid from the wages? Or does they belong to the normal army upkeep?"
I'm pretty sure it goes on army upkeep
"Is the size of the bodyguard related to the amount of stars of the general or the experience of the unit?"
the older, the bigger the BG up to a set maximum; leaders and heirs have bigger BG compared to other generals
