Hello! I also have a 2008 Mac Pro and was in the same situation with red LEDs at startup. There are some reset micro switches integrated on the logic board, at least two of them. You might want to try them, they're place and function are listed in the service manual, if I remember correctly. Also check the ram slots and the whole riser module itself, you could replug them or blow the dust off the pins and sockets. Ok, this might solve your problem, but didn't do it for me with the same symptoms.
What really was is mind blowing, and it's a real drawback of EFI not being accessible to the user at lower levels. I discovered the culprit by accident. I pulled out all my hard drives for data safety, my Mac booted. There was some kind of a more serious problem with the hfs volume that i could repair with Macdrive in another windows PC. I put back the drives, and everything was back to normal. A simple partition error brought the whole system to its knees, exhibiting the same symptoms
My local apple service center couldn't say anything beyond what I described in the first part, they never had a bad Mac Pro since introduction. I was just about to dig up logic board replacement, and grind my teeth in anger because of the cost...
EDIT: I forgot to add that with the disks inside I wasn't even able to do anything as the fans behave abnormally and the boot process couldn't get started: complete halt, blasting fans, glowing LED-s. So booting from install disk to run Disk Utility was a no go.
As much I love Mac OS X and the beautiful hardware, a simple "checkdisk" type error produces a complete system halt and hardware failure symptom
I had exactly the same thoughts about why investing into a platform like this, etc... I agree that in the ppc days Apple was at the forefront of pro features and software. While I love my iOS devices, I am saddened by the fact that for cutting edge video workflow a windows pc is simply a requirement as there are serious compromises on the Mac platform in terms of performance and availability.