I received the new processors and put them in about a week ago. They work great! Temps are a lot more normal. There is still a slight difference in temps between the two processors but that is expected.
I’m positive the temps will go down with time. I read this article from someone who upgraded to the exact same processors as me. He states that his temps went down after a couple months. Apparently thermal paste needs to be “broken in”. It makes sense but I’d never heard of it before.
Also, I upgraded the firmware from the 2006 (MacPro1,1) to the 2007 (MacPro2,1) using a utility found on netkas.org. This allows the “About This Mac” box to show “2x 2.66 GHz Quad-Core Intel Xeon” instead of showing “2x 2.66GHz Unknown” for the processor specs. **EDIT:** You can download the utility from here.
I took the liberty to encode a Blu-Ray movie to H.264. It worked fantastic! Temps were in the 80°C. It was a lot better than the last time I tried with the old processors! (Last time temps shot up to 100°C and the fans were going at full blast. It sounded like a jet taking off!!). I was very pleased with the encoding speed. On my previous Quad-Core Hackintosh, 1080p would encode at about 6 fps. This was encoding at about 24 fps!! That is amazing in comparison to my Quad-Core i7 Retina MacBook Pro that gets about 27 to 28 fps!
All in all, this 2006 (now converted to 2007) Mac Pro was well worth it in terms of performance and price.