First, the ROM socket is 2 pins larger than normal! Is this normal?
Yes it's normal, it supports 1mb kickstart roms.
The ROM that came with it was supposed to be a 2.04, but it appears to be DOA so I dropped in a 1.3 and a 3.1 positioning the ROM towards the front of the motherboard and it works, sort of.
The 1.3 thinks about it for a bit and comes on up.
The 3.1 GURU's but when I click the left mouse button it pops up the insert disk screen!
The 3.1 ROM I'm using is for a rev 6A 500 mobo. Is this the correct one or should I be looking for a different ROM?
If it's coming up at all then you've got it plugged in properly (when the socket is larger than the rom then you leave the pins free at the end with the notch).
I've also had problems with guru meditation when turning on, I don't know the cause. It's a wonder that any of this stuff still works at all.
A rom from a Rev 6A should be fine. The A500/A2000 kickstart roms were all the same. A500 rev 3 & 5 just need a wire added between pin 1 & 31 of the rom (the old German A2000's need this too, the more common B2000-CR's don't). Upgrade roms always came with the wire attached & you had to remove it if you didn't need it. I had a rev 5 and had to remove it anyway to use a kickstart switcher, I soldered the wire on the motherboard instead.