Here is a pic of the rom, if you look carefully at the picture you will see in front of the ROM that there is 2 pins empty.
That is a picture of an a600 motherboard, they either have 40 pin or 42 pin sockets. I can't tell from that angle as there are too many optical illusions going on with the lighting and the angle. Here is a less insane picture
http://www.bigbookofamigahardware.com/bboah/media/download_photos/a600mb_rev15_2.jpgThis is a rev 5 a500
http://www.bigbookofamigahardware.com/bboah/media/download_photos/a500mb_rev5_3.jpg, which only has a 40 pin socket (the a500+ has a 42 pin socket).
Normally you would only use 42 pin sockets for 1mb kickstart roms (i.e. 3.9 etc), 2 extra pins means there is up to 4 times the capacity. If he programmed each part of the rom with the same contents then you may get away with leaving the extra pins floating (1mb rom would need two copies, 2mb rom would need 4 copies). I'd personally bend the extra pins up and solder a wire to ground to avoid any doubt.
I believe the extra pins that don't go into the socket are the ones at the end with the notch, because when you go the other way and put a 40 pin rom into a 42 pin socket then these are the pins that are empty.