Grimjaw is spot on as to why you can combine multiple Militia into a 2 unit brigade. You would need to change all the militia unit files as there is a unit file for each state. Note that in the vanilla game uses the State volunteer units as militia and not the militia unit files. So, for the rebs, units 172 to 185 rather than 186 to 199.
Regards your point 3 .. this is tied in to how element names are assigned.
For single element Units (even if they can be brigaded into multiple element units) then the game uses the custom name in the Unit File for both the unit name and the element name. If you have a multiple element Unit then the custom names from the model file are used for the element names. So for single element units you are pretty much locked in to the Unit Name being also the element name if you want some sort of historical accuracy.
This thread
Link talks about it a bit