Since this looks like a road bike build, you could go with either 140 or 160mm disks, 160 being more common and perhaps cheaper. The TRP Spyre brakes don't already come with rotors? If they come with adapters, see what size rotor they will accommodate and go from there. Personally, I'd opt for 160s.

You'll have way more choice with 135mm OLD hubs. Get 6-bolt standard hubs, not "centerlock." Rotor alignment should be standard, but I am not familiar with Boma and 130/135 convertible(?) rear introduces complication to the point that I wouldn't say for sure. Cup and cone can be sealed bearings, but they are adjustable; cartridge bearings are good or not, are replaceable. I'd not base hub choice on bearing type -- they both work.

I can't advise about gearing without having something to compare it to -- what's gearing on one of your normal size bikes which you like? Otherwise, even with the smaller wheels, I'd be tempted to go with a compact crank, 50/34 or a 11-32 cass. Maybe both. But only because I prefer lower gearing.

Good luck!