Sounds a lot like the issues I have with my rev2 Grex.
When it _does_ boot a sysinfo speed check shows it either:
1) Is running as a 68ec020 at 25MHz (ie stock cpu at accelerator board clock)
or
2) Is running as a 68040 at 14MHz.
In both cases WhichAmiga fails to detect the PPC side, the Voodoo never displays anything (or even gives a signal to activate the monitor) and booting up takes forever.
I suspect either the manual jumpering of the rev2 logic/bus board is done incorrectly, or something is shorting. I'm loth to remove the manual jumpers to find out though.
Funnily, when there are no PCI cards in the Grex everything runs fine, at normal speed, and the PPC cpu is identified OK by WhichAmiga.