Exactly, I forgot about this. Actually, for now, just use a constant manual fan speed of 100% (full speed). Just choose a manual percentage and disable any "auto" settings and fan profiles. Then see if you still get crazy temps.Try creating a personnalised fan profile in MSI aferburner and get the fan to kick in as soon as it starts generating heat.
It does sound like something is faulty though...
edit. missed some posts, sorry above is not relevant anymore
On the other hand cooling is difficult to fail, as long as it's all clean.
High voltages generate more heat so it would be best to confirm that your running stock values.
I'm guessing the hugely decreasing GPU core clock changes are from the loading screens of 3D mark or something similar - completely normal. I still do see some small fluctuations during seeming normal 3D use, however it seems pretty minor and normal for the auto-boost GPU clock stuff of modern GPUs. Having said that, I used/use a custom bios for my 3 780 Tis (2 EVGA Superclocked reference versions, and 1 ASUS DC2 Overclocked custom version) as I noticed little stutters, and such, which matched up absolutely perfectly with all the small dynamic GPU-core clock fluctuations that the new cards so stupidly use. However, this does not seem to be your issue since notice the stutters at a very specific and repeating interval.
Blast the fans at a constant 100% while redoing the tests (with monitoring software running).