I’ve had one of each (USA Pro Mod, MIJ Pro Mod, MIM Pro Mod, custom shop.)
My thoughts:
USA - I think you find these the most consistently good. Nice body woods, fretwork, found my USA neck to be slightly bigger than the MIJ, MIM necks which actually fits my hand a bit better. Really hard to find these days and are overpriced on the used market IMO
MIJ - the rolled edges on the fretboards make these probably the best necks, fast and slim. Bodies and resonance are ok and varied a bit between models I tried. Only one that came with a nice SKB case.
MIM - varies between years, the most inconsistent of the bunch so definitely try before you buy. Some gems and some stinkers. My current one is a 2016 SoCal. It’s middle of the road but seems to do the job for me.
Custom - At one point I had a Music Zoo flat black San Dimas with a HS config. It was definitely the most solid and well built, immaculate fretwork. But something just didn’t jive with me and it always sounded a bit dry to me. I ended up trading it for a MacBook Pro which I still use after 6 years lol
I would never buy a custom again unless I can play it before buying.