I installed custom burned 3.9 ROMS in my A4000 because I wanted to eliminate the double reboot. It wasn't as compatible as the 3.1 ROM. One of the things it wouldn't do is the double-mouse button on boot up plus LoadWB command, a very useful way to get into workbench when something is stopping your amiga from booting.
I put back the 3.1 ROMS.