You may check rear of motherboard at 5-pin power connector, I once had cracked solder joint because this socket gets much action over years. So I had jamming machine, but once I resoldered it, it booted fine. Ofcourse this is just one of many possible failures. I don't think this is in any way related to custom chips, but 2Mb Agnus is really incompatible with early mobos.
Also did you have 512kb RAM expansion connected? If not, try one, because if someone made 1Mb chip RAM hack on this board, it wouldn't boot without additional RAM installed. Good luck!
