It Looks like the IAT sensor is on the inlet of the SC and not on the outlet. I mean I don't see it located anywhere else so it probably is there.
Therefore it won't pull timing, adjust fuel, etc with regard to temperature.
This basically disables a ton of stock safety features from the stock computer. Add to that the knock sensor being disabled and you get knock which breaks pistons. CRAZY.
The knock sensor retard rate can be adjusted and changed for various rpms as well. It will take quite a bit of time but I'm positive I can make a good tune.
The first thing I will ask you to do is verify the position of the IAT and if in the inlet then to pull that IAT sensor out of the inlet and put it into that black outlet pipe. Then we'll know what temps we are dealing with actually going into the engine. You can do this easily with a simple mod to the sensor. We take the sensor and file off the ridge at the end that retains it in the intake tube, then we take a die from a tap and die set and just thread the body of it with some threads. Doesn't matter what tap/die combo you use as long as it fits on the sensor body enough to make threads.
Then you take the corresponding tap, drill and tap a hole in the black intake pipe. Use a nice fat o-ring and or piece of silicone rubber with a hole in it to make a gasket to insure sealing.
These sensors threaded into the pipes have so far withstood 15psi boost no leaks so you should be fine on your SC system.