Hmm. I haven't scrutinized the air temp correction tables, but in theory you should be able to just rescale/retune them -- they are probably affecting timing more than fueling, as regardless of measured temp, it should still be reading a greater airmass (although I'm surprised folks aren't hitting 5 volts with some decent boost).
Of course having the ECU actually respond to actual (post IC) temps would be preferred... Does it tend to run lean, rich, or just pull timing?
Anyway, so long as you have post IC temp readings to monitor and log, even manually from an outside gauge, you can probably just re-tune the adjustment tables to get everything closer to the desired ballpark.
Is the problem definitely one of measurement? I had thought the major issue with the stillen kit was that the piping design was just poor for flow beyond a certain level of boost