I've used xtrememicro once for a pair of E5 v2 xeons and had no issues, I was also looking at a weird x5679 cpu for my mobo, a z8na. he came straight back and said it would not work as my mobo is limited to 95w cpu's and the x5679 was 115w.
As always everyone's experience is different.
I had issues ages ago with pair of Ivy bridge based xeon's not liking USB 3 on my Z9PA. I ended up turning off usb 3 completely in the bios and that would allow me to boot and run without problems. You could also be hitting problems with a couple of the oprom's, especially storage and nic...
I've got a pair of early B0 Sandy bridge E5-2665's, they've been running in a folding rig for 3 years 24/7 and haven't missed a beat however YMMV and as Patriot wisely pointed out I can not flash the bios to a newer one as it breaks compatability with the chips.
Hyper 212's work just fine on square ILM 2011 sockets, I have a pair running on one of my folding rigs. For narrow ILM, which it sounds like you have, you are out of luck - you will need a pair of heatsinks from either supermicro or intel.
Depends on whether you can a: afford to run them and b: can you afford to upgrade. personally I would look to sell it off and look for some thing newer. If you can afford to go new I would look at some low tdp E5 v2 or v3 cpu's , if you need to go used I'd look at a pair of L5640's or low tdp...
v3 haswell xeons are not being released for the current lga 1356 platform, you are limited to sandy bridge or ivy bridge.
v3 requires the lga 1356-3 socket, its not pin compatible with older 1356 based boards
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