If you are going to do a rebuild for a 4000, why not improve it a bit.
PCI allows access to a plethora of add-on cards and expansion ability that, yes, will require drivers, however, at least it is there.
Buffered serial to go past 56k using standard 16550 chips would be great, or a USB 2/3 stack to use plugin serial as a replacement instead.
Oh, and how about a real HDD controller that's not in PIO mode. Well, with PCI, you could always plug one in with a cheap card I suppose. Just need drivers.
A FPGA unit would be fantastic also, hooked to a clock port or something?
The original hardware was so limited by the start of the spiral down and people were waiting with baited breath on a hardware refresh with AAA for so many years and nothing was done.
Could be a real opportunity to do something really different and in the AMIGA spirit.
Besides, aren't the chips no longer made? CIA etc??