This is going to be a process of elimination and it sounds like you're on the right track. There may be a circuit or two that doesn't go through the fuse panel. Check your new wiring diagram to confirm this or, worse case, trace the wiring of BOTH sides of the ammeter. The horn, cigar lighter, and others may be wired direct and not go through the fuse panel.
It is possible that one of the ammeter terminals is grounded but not very likely unless they removed the guage cluster for painting. With a direct short like this there also may be burned or discolored wires that may help point you to the short.
Good hunting! Keep us posted.
