The red screen can be the ROMs, OR any card that is acting up. Best routine is to remove ALL cards, and see if it will re-boot. This should include anything connected to the clockport too.
If the ROMs were inserted incorrectly, they may well be fried - it doesn't take much. The 3.1 OS is a worthwhile upgrade, so go for it. Only a very few hard headed gamers will try to argue that case.
I wish the OP luck getting the machine up and running again....
