Coincidentally, I was reading through my copy of the Commodore-Amiga 2nd Annual Developers Conference Notes (from 1986) this morning.
There are two articles which cover installing Kickstart EPROMs in 2-layer A1000 boards. There are several different methods, two of which remap the old Kickstart WOM/RAM to $F80000 (you use an AddMem program to manually add the memory at $F80000-$FBFFFF).
I'm anyone wants I can scan or type up the relevant pages. That should help a lot with your understanding of what's involved and the different options.
Would there be any chance to post this information, still?
