The first think I would do is to goto Pindelski's web site and link the the Apple Service Manual (http://pindelski.org/Photography/2013/07/08/mac-pro-2009-part-tbd/ and browse that to see if there's a process you can follow to determine what your issue is.
I'm just about to upgrade my 2nd MP4,1 today and hope it goes well for me. I will be upgrading to the X5670 processors as well.
The upgrade of my early 2009 MP4,1 with 8 core 2x 2.26 GHz E5520 processors to a MP5,1 12 core 2x 2.93 GHz X5670 processors was a complete success. At this time this MP5,1 only has a 1TB 7200 rpm internal disk for the OS 10.9.3, 4 GB RAM (2x 2GB sticks) and a stock NVIDIA GeForce GT 120, and its Geekbench 3 64-bit Multi-core score after a 10 hr stress test gave a high Top Score of 26111. The original MP4,1 Geekbench 3 64-bit Multi-core score was 13525. Cinebench R15's CPU Rendering score went from 750 cb to 1404 cb.
The above was the most challenging part of my upgrade... now onto the easy bit.
I will be adding 64GB RAM (8x 8GB 1333 MHz sticks from OWC), a 480GB OWC Mercury Accelsior PCI Express SSD card for OS, replacing the NVIDIA GT 120 graphics card with a Sapphire HD Radeon 7950 for Mac Pro, OWC's 2x 240GB Mercury Electra 3G SSD 2.5" for AE cache use, 2x 2TB Seagate 7200 rpm RAID-0 for Project data, use the current 1TB 7200 rpm internal disk for OS clone and use existing Time Capsule for Time Machine backups. With this final hardware upgrade I expect a Geekbench 3 64-bit Multi-core score of around 27500 and a much more capable and responsive system.
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