How about you do the diagnostics instead of trying random things? Run AHT/ASD and see what is really going on.
AHT/ASD:
You need an Apple OEM GPU (HD 2600XT, 8800GT, Quadro FX 5600, GT120, HD 4870/5770/5870) to run AHT/ASD. AHT/ASD can be used with PC flashed GPUs, but will fail mid test with a sensor error when the GPU sensors are tested. Non flashed PC GPUs won't work at all. You need to boot completely vanilla, no OC, to use AHT/ASD.
You can get AHT links and instructions on how to install it on this GitHub article.
AHT, you need 022-4831-A.dmg:
Apple Hardware Test Download Links. Contribute to upekkha/AppleHardwareTest development by creating an account on GitHub.
github.com
The ASD version that you need is 3S149. The AHT instructions are valid for creating an ASD USB key and Apple provides an installation PDF inside, after you mount the disk images.
ASD, you need 3S149:
As an information architect, these are a few tools, articles, and miscellanea that I find useful.
www.loremipsum.info
For people that have an early-2009 cross-flashed with MP5,1 firmware, you will need to run the MacPro5,1 versions of AHT (022-4831-A) and ASD (3S149).
Your Mac Pro have a problem(s) for a long time, you are working around instead of diagnosing and repairing it. If you are going to test anything that you can think of, you don't need to ask me here.