I was actually quite discouraged when I upgraded my GPU to a GTX980 and threw a loaded Amfletec Squid into my 5,1. The first thing I noticed was the SMC reacted to that by raising my PSU fan to about 850 rpm and PCIe to about 1050 rpm from their default 600/800 rpm. It was noticable to me because I never really heard the fans before that but I'm used to their new default now and it's not too bad.No problem. It's nothing wrong to do that.
The W3690 rated up to 101C (diode temperature, from the official intel diagnostic tool).
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From memory, X5690 even rated up to 105C. IMO, as long as Turbo Boost still active, there is no noticeable benefit to cool down the CPU to below 70C, but shorten the fan's life, and have more fan noise.
But if that make yourself more comfortable, then of course you can do that, it won't hurt anything anyway. I don't think the fan is that easy to break also, especially you only occasionally stress the CPU.
I'm a bit paranoid so I ordered all 4 Mac Pro fans for backup just in case any go bad in the future. I got a good deal of about $40 for them all and they look brand new.
[doublepost=1555720284][/doublepost]I'm still hoping to see the first person to hook up their 3rd party Northbridge fan with power from a PCIe card or an empty SATA port. If using a 5v fan you'd have to stepdown the voltage, perhaps with an inline resistor but it could be done. I think the advantage to that would be you could tuck the cable behind the backplane for a neater more permanent solution. That is after you guys get out of the testing phase and find a solution you're satisfied with.