I looked at the unit naming python and didn't see anything that was necessary to change but then my python understanding is somewhat limited. What, exactly did you have to do there?
The promotions... well, sure that's always going to be an issue but if spreadsheets are used to track that it becomes a lot easier to plot out and then once plotted out its much easier to go into the xml, search for the promos you need to adjust, and knock them off one by one. I wouldn't think that would take toooo long.
Also... note: I think you may be asking for too much from a combat class definition on some of those limitations Nimek. Combat Class can create sweeping unit guidelines but many of those you noted would have to be put on each unit individually anyhow as there aren't controls for establishing them on all units with a particular combat class. (like build with food, can't attack, etc...)
I'd love to be able to make tags that influenced units across a combat class board but unfortunately its a part of a data structure that can't be modded without messing up the core exe processing apparently.
There are a lot of ways you can call up a combat class as being a factor in something however, for example, combat bonus or penalty vs a particular combat class.