im not sure if the cards would be able to take advantage of updated speed.
No, not at all. Probably it'd be wise to stick at the current speed for compatibility reasons.
My intention in talking about PCI/e was that once you pick up this task you should do the job thoroughly - without adding too much complexity, PCI soft cores are around.
Step 1: You could redo the Buster, maybe speeding it up a bit, but most of all removing the bugs.
Step 2: Integrating a PCI port opens the door for replacing the daughterboard with one carrying any mix of Z3, PCI or PCIe slots, connected to the Buster PCB by a ribbon cable. Better PCI performance without messing with Z3.
Step 3: The daughterboard has yet another connector for hooking up an accelerator board directly to the PCI world. Except for the Bvision port danbeaver mentioned all other solutions require the - fast - accelerator to go over the - slow - motherboard bus to reach a - fast - PCI busboard. Obvious where the bottleneck sits.
At the same time the '030-to-PCI bridge we built into Buster starts to work the other way around, interfacing the accelerator to the motherboard, removing some complexity from accelerator design.
Step 4: Why use an expensive and hard-to-get 68060 CPU? Better take a cheap, fast and cool(!) ARM CPU with integrated PCIe and 68k emulation in firmware. You won't see a difference except that it's faster. The 5V adaption problem has already been solved with the Buster replacement.