Machine it first, and finalize the lower. Build it and test fire it to make sure you machined everything right. Once it fires, rip it apart and paint it.
It would suck - SUCK - to machine it and paint it, or worse yet, paint it then THEN machine it - to find out that something was off, and you wasted $35 for 4oz of Cerakote.
This is the 3rd one I've done with Cerakote, and I haven't masked any holes in the lower or upper. Everything goes together great, with painted holes. This stuff goes on at 0.0005"~0.001". 5 TEN-THOU to 1 THOU. It goes on pretty damn thin. <thumbsup>
I was heavy on that Snow White, and the only thing I thought I messed up was not cleaning out the safety selector hole before baking. Baked it, installed the safety, and it loosened up with one drop of lube.
Get after it, man! <lmao>