Just installed the GeminII for my E5200. CPU temps were (and are) fine, basically the same as with the Q6600 stock cooler, but the chipset was (is) starting melt pretty much, it rose to 94 degrees in temperature within 30 minutes of the computer being turned on, without any particular load. I installed a temporary 120mm fan - Antec TriCool at minimum speed to keep it at least somewhat silent - on top of the "front" edge of the Geminii to try to blow some air downwards on the chipset heatsink. But of course as the drive cage blocks it for the most part and a cable mess takes care of the rest, it doesn't get much cool air to work with.
Running Prime95 now, the chipset is already at 87 again.... probably still going to raise as well. How high a temperature is "safe" for the chipset anyway? With the Q6600 cooler, which I would not have thought to give much airflow to the chipset heatsink, it didn't go over 60 even when overclocking. How do you folks keep the chipset at reasonable temps with the GeminII?
To top it all off, the system as a whole is still anything but silent when in a quiet room. Can't say which fan makes the most noise, but it's one of the two "stock" fans, since adding the TriCool made no difference to sound levels. I do have a silent Nexus fan on order to replace the front fan, but I'm sceptic as to how much of a difference it'll actually end up making.
You may want to try reseating the chipset heatsink and using some AS5 on it. Since it's secured with spring loaded push pins, it can rock back and forth pretty easily and actually lose contact with the chip and mess up the thermal paste. This happened to me on a similar build and I had to replace the splattered thermal goop with AS5.
Also you should make sure the cpu heatsink isn't coming in contact with the chipset heatsink and nudging it up off of the chipset.