1. Why didn't you the different colours between the ST1 Enterprise and ST2 Enterprise?
The Ship was not repainted till Star Trek 4, the only changed to the TMP and TWOK paint job is the battle damage.
2. In BC, why is the ST1 Enterprise using the battle damage textures on the secondary hull from the ST2 Enterprise?
Not sure what is going on there. I have deleted my install of the ship and installed using the uploaded file RAR file. And works ok on both high and low res. Try copying the BCRefitA secondary hull texture to the BCRefit folder.
One little note is the low secondary texture for TSFS Enterprise has no damage on it. It will be fixed in further releases of the pack but for now you can either live with it or resize the high version to 512 x 512 yourself.
3. Why didn't you replace those yellow textured parts on the warp bussard colletors with something that actually look like lights, on any of the Enterprises?
I'm happy the way they are. If people don't like them feel free to edit them.