When you say the base is shortened, do you mean the plate, or the plate holders. I did notice that I had to push the plate brackets in as far as possible to get the push-pins to line up. Is the thermal tape think enough to compensate for the raised SMD chips?

I had to play around with the thermal tape a bit to try to get it as flat as possible. I'm wondering if handling the tape (I fixed it after both side of the tape were off) is the culprit for the bad temps.

EDIT: I ran prime to check the PWM area, and the temps were still climbing when it had hit around 65-70. I shut it off because I didn't want anything to burn out. When I get home later today, I hope to have this PWM thing fixed.