The EPROM's are for diagnostic/debug only, you can even take them out and set proper jumpers - card will boot.
Jumper settings:
http://www.amiga-hardware.com/showhardware.cgi?HARDID=234 As far as I know it's not possible to upgrade CPU from 040 to 060 just by replacing CPU. You have to replace whole CPU daughter-board.
But never tried by myself, so I can be wrong.
