Hello and welcome nathan.

I have not built this kit. But, I put some Tonerider Birmingham humbuckers into my DSCM-1 build last year. I think I had to cut back the corners of the screw mounting section a touch, to make them more circular, so as to get them to fit into the humbucker routes. But no major work was needed. I think the EX-1R should be similar.

Some pups do have different wiring, but generally would still work with the Pitbull parts. If you stick with humbuckers the pots would not need to change - I think humbuckers are usually put with 500k pots, while single coils are generally with 250k pots.

I'm not sure about your paint query.

Good luck with your build.