well when fender first bought them out the general consensus was that jackson went sharply downhill. my opinion is that since then theyve slowly but surely worked their way back up to building high quality instruments, 06 onwards theyve been making some really good stuff
No differences in instrument quality. Better distribution. All good things I feel.
The have more resources now for quality control, which is only a good thing.
The years before the Fender era, and a few years they had some problems with QC, even for their custom shop, but nowadays they're as good as ever.
Jackson KV 2, Jackson COW 7 (both in B), Jackson Demmelition V
Bogner Überschall (blue rev)
Marshall 1960B Vintage (2x V30 & 2x G12T75)
TC Electronic G Major
BBE Sonic Maximizer 422A
Weber Mass 150w
ISP ProRackG
T.Racks Dinopower
It depends on what level you are looking at. The low end guitars can sometimes be in really sad shape. I think the Japanese ones are better than some years, and one of the weak aspects in the tremolo, but I hear the OFR can be dropped right in as a replacement (and considering the price difference between the Japanese and USA guitars, it makes that upgrade actually worthwhile). Custom shop is custom shop and at that point it is more a matter of who is building the instrument.