I'm not sure if the HD HE has changed since I purchased mine, I'll give Whipple a shoot and get that clarified.
I do agree about the fan location, I've been looking at that for a long time now.
I almost want to put four smaller ones in the back of the HE and cover the whole surface.
Also $100 is $100, could fill up the tank one and a half times. LOL
The IAT reading is coming from the PCM so it's the manifold sensor. If I do a hard pull that IAT reading will jump right up.
The factory PCM IAT reading is taken at the mass air flow sensor, before the supercharger. Now the Whipple kit does have a IAT sensor added to the manifold that you pin in to the PCM I believe pin#59... Your temps seem to be in line with what I would expect from an IAT1 reading at the MAF, not in the manifold.