Are you using the stock pin2k computer? Does your cpu fan spin when you turn it on? what happens after a few minutes does it boot? Maybe there is something set in the CMOS and it has to time out and then continues booting. You said you replaced the power supply. perhaps the cmos was set back to default?
Quoted from WeirPinball:Finishing up a SWE1, but the computer seems to have trouble booting. Doesn't seem to boot unless I leave it on for a few minutes, then turn off the computer and restart. Tried reseating everything in the computer, pulled the prism apart and put it back together, new power supply. It isn't the monitor, because no lamps/sounds come on. The caps on the MB are fine, not leaking. Any help would be greatly appreciated.
Scott