The A1200 case would lend itself to a motherboard with something like the old Western Digital layout that Compaq or Dell used on their office machines like the Dell Optiplex GX series (God I am sad to be able to recall all this crap) where all of the I/O ports are in a line, that way you wouldn't be hacking the case about too much.

Another alternative is an ITX Shuttle mobo.

I'm not a fascist when it comes to Amiga or PC modding, to each his own, if you are gutting the Miggy, I might be interested in the old innards...

Merlin