transmission clean up and paint

If you are set on painting it, I would actually talk to the builder first and let him know your plans. Degreasing, wire brushing, and scrubbing are all ok before the rebuild but you don't want it to sit around too long before disassembly and rebuild in case water gets inside and starts rusting the steel parts. Also, some builders use a parts washer after disassembly to quickly clean the parts. If they are going to run the case and tail housing through a parts washer you probably don't want it to have fresh paint on it as some may come off. They may let you take the case and tail housing for a good scrub after disassembly.

Painting after the rebuild is a good idea because as said above everything can be very clean after the rebuild, but then you'll need to do a careful clean and degrease again before paint. There is often finger prints or drips of trans fluid on the outside after handling the parts.

Finally, make sure to tape off any openings before painting. Don't really want paint on the inside.