There's no reason why the system would NEED the original board to work. What you have going on here is more than just a motherboard failure.
Be sure you give the RAM a complete test run with Memtest x86 (I run it from Download Hiren
, burn to CD/UFD then run it and choose the memtest option) - let it cycle at least twice to ensure that you find any problems immediately apparent with the RAM. Letting it run overnight is not a bad idea either.
You also need to investigate things like heatsink / thermal interface, since you had to rebuild the system, did you use an adequate amount of the compound to re-attach the heatsink to the CPU? Sometimes if they run too hot, they can slow down (even the AMD chips)
Also, using the same Hirens boot CD I linked, run the hard drive test gwscan from the hard drive tools menu. Do a full scan on the drive and see if it picks up any errors.
Something tells me that one of those two tests will find something wrong, but if it doesn't, let us know.