Do we have to currently own both to post? If so, I apologize ahead of time.
I currently own two MIJ Charvels. A SoCal that I swapped the body out for a SanDimas body, and a Wild Card #4 Dead Calm Aqua.
I've owned a USA Charvel, and have played a bunch of them. In many cases, right next to MIJ ones.
There is not much difference. The differences have been mentioned already. The MIJ have rolled fingerboard edges, a different(thicker and darker) finish on the neck, and seems to me nicer fret work. The MIJ necks feel faster, too.
One pain in the ass thing about the MIJ San Dimas(to me), is that the pickup routes are so shallow and they are direct mounted. This means that the pickup is jammed up close to the strings and you can't really adjust it. I routed my San Dimas deeper and installed pickup rings, and I'm happier for it.
Of all the MIA and MIJ Charvels I've played, I would seriously recommend you play before you buy if at all possible. They can be hit or miss. Both versions. I don't think I've found one to be more consistent than the other in this regard.
Also, do not forget to try changing blocks to steel or brass. This makes a bigger difference than pickups. Steel for brighter, harder, louder, more PING, more highs and lows. Brass for filled out musical mids that have more bloom and more bell like.