The only real problem I had was with the air tanks. The annie chassis has longer steam chests, which interfere with the 2nd generation air tanks. I cut the air tanks back to the first mounting band. The tanks are made of four pieces - two sides, and two end caps. Once I cut the tank back, I glued the end cap back in place. once that was done, the air tanks went right back into place using the original mounting holes. That was the only physical problem with the changeover.
As far as the paint, I completely disassembled the loco, pulling the parts off the original chassis that I was going to need, such as the supports for the boiler. Everything got cleaned of grease and oil and primed with Rust-Oleum 2x grey primer. when that was dry, It got several light coats of Rust-Oleum flat black. We've had a lot of very windy days lately, and I live in Arizona, where dust is ever-present. So when it was just about dry, I moved the pieces outside and set them where they would acquire a coating of dust. After that I started painting the trim/accents/handrails. That is still being worked on. I haven't hooked up the light, or the smoke unit yet. I haven't even installed the stock smoke unit back in yet. I'll take care of that when I decide which decoder/sound card I'm using.