Dan.... happy to help. Wanted to give you a bit more info:
In all of my experience with the Z400 v2 and Z600 v2 I've found that the official HP processors in the late QuickSpecs for these two boxes work fine. As I noted the X5690 was never officially certified for the Z400 v2 but it has worked every time. I used to think it was the best for that Z400 workstation. I did try it in multiple Z600 v2 workstations as a single processor but never succeeded.
I've recently learned that the W3690 that is officially certified for the Z400 v2 actually likely is the better choice for that box. This is because it has an unlocked multiplier whereas the X5690 does not. Thus, it can be overclocked with the Intel XTU utility that Bambi and Brian use so successfully as described in their posts. There is another utility for doing this type of overclocking, ThrottleStop, which is well respected also. Here is a YouTube video on that, and I'll experiment with it a bit on the Z420 v2 and Z620 v2 boxes. HERE is a link: https://www.youtube.com/watch?v=MewSdpzQVjU
He assumes you know to click "Turn On" at the bottom for testing. This utility is being supported by the author quite well, and is W10 compatible, and has no cost.
I still think your current plan is best, but if you happen to have one of those processors around you might like to try it in your Z600 v2 as a single processor, overclock it, and report back.
The X5675 PassMark average CPU score is 6386 if one and 11797 if two. W3690 is 7185 without overclocking, and X5790 is 6800 if only one is being used. The dual QPI links in the X5690 that let you run two in the Z800 cost you some speed, as you can see.
A bit related..... for those who want to load in a more modern video card with need for an 8-pin PCIe supplemental power adapter the use of adapters using 15-pin SATA power feed in is discouraged in favor of the good old 4-pin Molex power feeds, with a good adapter as shown below. There are a lot of cheap substandard ones out there... here is an A+ version which I have clarified for what is going on. You'd want to use 4-pin Molex feeds from two different power cable sets coming out of the HP power supply if possible:
