... but I also noticed a modification to the board. It looks like an added transistor just below Denise, but I don't know what it represents.
I also noticed it some Amiga 500 repair video's on Youtube, but it is never pointed out and explained.
It's the DTACK fix for the earlier Toshiba Gary version. It was factory installed on early rev5 boards because some of them might still ship with the earlier Gary chip. If you have the corrected MOS/CSG Gary version you don't need this transistor, but it won't hurt anything either.
Later rev5's (when stock of the Toshiba Gary had dried out completely) obviously dropped this factory mod but introduced a different (not 100% essential) one (a 68 Ohm resistor from 68000's E clock line to the first corresponding CIA pin - a trace must be cut to implement the fix).
