First of all, NEAT!
Now, as others likely wonder, why the 040? Why not flat-out PPC? If 68k is necessary to get started, why not TG68 or WF68K00 inside that FPGA, and then remove it later when PPC is going well?
I have ideas for PPC accelerator as well, though I'm not sure how well it will fit a case the way I'm thinking of it. But I wouldn't have a real 68k chip. Without a PPC, I'd go all FPGA and some slots, and have whatever the best softcore 68k is in the FPGA. Perhaps even the Natami 68k if things could be arranged with them. (My idea of course is not anywhere along to be worth their time asking) Soemthing like Majsta's idea with SODIMM, perhaps USB and some other connecters for things that work well inside FPGA. (IDE? SCSI? Ethernet? etc) Much anything beyond the FPGA and connectors would be a removable module, industry standard module, to buy the PPC part form someone else and save me the trouble.
SODIMM on my FPGA-only board would only really be fore the FPGA's sopftcore 68k. PPC module has it's own (and probably much faster) RAM.
Any plans for something like an MXM graphics slot?
I'm very curious to see how your project goes!