Another upgrade you can do on the 2006 that I have done to mine, is when you get the x5365 cpu's, you can also get a pair of cpu heatsinks from a mac pro 2008 3,1. They have a LOT more cooling ability than the 2006 ones, including the air dam that helps get more cooling to the lower cpu since its the hottest one. The only caveat is that the lower heatsink temp sensor wire is too short, so you will need to pry the temp sensor off the old 1,1 heatsink, and re-glue it to the 3,1 heatsink so the cable will reach the plug on the motherboard.
The reason I did this, is the 1,1 cpu choices never were higher than 80 watts each, so its heatsinks were made to match that. The x5365 is a 150 watt cpu. Since real 2,1 heatsinks are wierd and very hard to get, the 3,1 ones work fine. The 3,1 also had 150 watt cpu's as an option so it has the triple full length heat pipe setup on its heatsinks.
Last point, everybody that upgrades their cpu's in their 1,1's, I really hope you remove the northbridge heatsink and repaste it. The 10 year old paste on mine was almost totally dried out, and with fresh arctic silver 5, my MCH temps have dropped by 10c or more.