EDIT: FOR FUTURE READERS THE INFORMATION BELOW IS FOR THE Z600 VERSION 2 WORKSTATION, WITH THE LATER BOOT BLOCK DATE OF 01/07/10, WHICH CAN BE SEEN IN BIOS.
You want to search eBay for the less expensive 463990-001.... you're missing that zero before the hyphen. That is the "mainstream" 95W Max TDP heatsink/fan you want. The 463991-001 version is for the hotter processors, and is the "performance" heatsink/fan for the Z600/Z800. That is much less common, and thus more expensive. Note that a hotter processor does not necessarily mean it is a better performing processor. Sometimes increasing the voltage to a processor is the only way to increase its performance, but the trends always have been that faster and cooler is better than faster and hotter.
1. You can make them electronically equivalent by cutting out the ground jumper wire from pin 1 to pin 5 on the white plug-in end. I'd just buy a second 463990-001, which is what I did.
2. Let's say your Z600 came with a 463990-001 over the first CPU socket, and you had a spare Z400 heatsink (which virtually always are rated for the hotter processors). Then I'd get your two processors in place, and do the bend-down trick of that Z400's "performance heatsink" metal air deflector. You know about, and try that keeping the wiring as is. If you get an error message I'd then cut out the jumper wire on the Z400's plug, but I'm quite sure that you'll not see an issue.
3. No, because the Z400 performance heatsink/fan can only fit over the second processor socket. There is just barely enough room there for that if you bend down that metal air deflector a bit, but for sure it will not fit over the Z600's first processor socket. The idea behind that experiment I did was that if you were going to run two matched 130W processors in a Z600 then this would be a less expensive way to have two performance heatsinks/fans. One 463991-001 over the first processor and one 463981-001 over the second. If you look up the Z400 heatsink on eBay under that part number you'll see a few with more black plastic on the top and a black plastic rather than metal air deflector at the rear of the heatsink.... the metal deflector is easier to bend if you choose to go that route.
4. I would not risk it....... if you end up with two 130W processors I'd personally spend the money and do the trick I detailed in #3 above to keep total cost down. You know how to do the wiring spoof if you wish, but I would not recommend that. Just so you know..... the cooler more recent 95W processors are very fast, and some of the older hotter 130W processors are actually lower performance than the more recent ones running at less wattage.
5. The most recent (and last) QuickSpecs for the Z600 is v51 from 11/21/13, and this lists all the latest official HP approved processors for the later version of the Z600. You want to be in the highest GT/s QPI category which is 6.4 GT/s QPI. You want to be in the highest memory/processor FSB speed category, which is 1333MHz. You want to have the fastest clock speed possible which is 3.06 GHz if it is a hexacore processor or 3.20 if it is a quadcore. You want two processors, in my mind. You want to fill all 6 memory slots with identical 1333MHz proper HP ECC memory (either unbuffered or buffered, but not mixing), for optimal memory performance.
The processors need to be chosen for either highest clock speed, or slightly slower but more cores total.
Thus, the two potential best processors are either the X5672 (fastest, quadcore) or the X5675 (slightly slower, hexacore). Both run at 95W Max TDP. These are for the Z600 version 2, not the older Z600 version 1. My two Z600 version 2 workstations here at home are one of each, and both are great. I cannot tell the difference. For the software I run most of the time I'd lean towards the 8 cores total and the fastest possible clock speed of the two X5672 processors.
I have the Kingston Predator M.2 PCIe SSD running in both, using the special instructions I have posted here before. I'm only recommending the official HP approved processors from that v51 Quickspecs, but if you want to experiment with 2 X5690 processors be prepared to spend big bucks.
There is no guarantee that any of the processors you mention that are not on the HP approved processor listings in that V51 or earlier Z600 QuickSpecs will work. Don't forget you'll need dual QPI links if you ever plan to run 2 processors. Use the latest BIOS.
I'm signing off of this thread now, and good luck with your project........ below is that listing of v51 processors: