I'm afraid this is going to be an unqualified opinion, because I've never tried it but . . .
. . . do all the internal(?) work that needs to be done first and paint/powdercoat after that. Reason being there's too much potential for damage to the finish if you do it the other way round. Some of the work you want done (boring cylinders) will require bits to be held in place, and that could necessitate things like vices. That's not to say the people doing the work won't be very careful, but it's easy to bump/ding/whatever a finish when you're handling freshly coated parts. Added to which, you can go to town cleaning the residue of any internal work with stuff like acetone when there's no finish on the outers. Your choices of cleaners quickly start to limit once you apply coatings. Oh, and if you're going to do stuff like boring and valves, make sure you get the head and barrel mating faces checked for flatness. Making absolutely sure they're flat before you rebuild could save you a lot of time and effort later on.
Having said all that, I'd be very wary about powdercoating cylinder cases. I can't find a recommended running temp for these engines, but given that they're air cooled, it's gonna be hot. Powdercoat in its raw form will start to melt at 150deg c, so you might find it won't hold up to the sort of heat that's generated inside the cylinders. But even if it does hold, powdercoat encapsulates the surfaces it's applied to, and that's not a good thing from a heat dissipation perspective. Again, you need efficient air cooling and as much heat out of the engine as quickly as possible; powdercoat won't help with that.
Hopefully someone who's done it can give you some better insight. I tend to leave my engines alone after they're vapour blasted because the finish is pretty good without anything on it and apart from darkening a little over time, it doesn't need any special treatment - that, and I never need to worry about whether the finish will be affected by stuff like carb leaks). If I were going to need colour, I'd be inclined to consider heatproof paint, rather than powdercoat.
Hope that kinda helps . . .