So my rev 5 A500 with 3.1 rom, only has one jumper lead:-
from pin 21, to pin 31 on the legs on rom chip itself, with the leg of pin 31 of the chip bent out so it does NOT go in the socket.
now, as far as i can figure, on the rev5 socket:-
pin 01 - Address 17
pin 21 - 5Volts VCC
pin 31 - BYTE-WORD select?
on the chip:-
pin 01 - Address 17/18
pin 21 and 31 are VCC 5Volts.
this may help tracing :-
https://www.amigapcb.org/ i know they only have the rev8 A500 board, but it's been enough for me to trace lines and figure things out previously.
so it sounds like something got a dose of 5 volts where it doesn't want it... i hope you can find it, and its an easy fix!
it would just double check my working - i'm about 3 whiskeys in so far this evening. but it sounds like Address17/18 got a jolt. i hope you've got a spare 68k chip , agnus and gary chip to swap out to test? give each of them the sniff test see if the magic smoke has come out...