since your motherboard is PCI-E it will have a 24pin ATX slot... so if you PSU covers all those pins, it must be a 24pin psu. I havnt used a PCI-E board, but if its only a 20 pin PSU, and your not using a 20 to 24pin adapter. Id imagine that may cause some problems.
if your positive that the motherboard isnt getting shorted to the case, then you can leave it in.. but when i furst build a new comp, i assemble it outside of the case, ontop of the antistatic bad, with a thin styrofoam sheet underneath(anything soft realy so the pins underneath dont get forced against the bench when assembling).
Disconnect everything from the mobo, so you only have the PSU connected. Also make shur you CPU Fan is connected to the CPU Fan1 connector on the mobo. Clear the Cmos again. unplug PC from wall and switch the Cmos jumper, leav it there for like 10mins, come back and switch it back.
start it up and see if it beeps. if not then you know its the Mobo, or CPU.. iv never started a comp without a CPU, so i dont know if it beeps without it in.
If it beeps add one thing at a time and start it up each time. Then add ram and the monitor to onboard video. then EIDE drives.