I am surprised you found the throttle so, suspect that's where I would have started. I have a few auto D1's and they have all been pretty good - though one of them could be very on fuel...
I can understand a large intercooler not really working with EDC, as AFAIK, EDC can't take account of it - its too simple a system - ( which IME, is why you need an external box to play with it ), it was a half way house to try and get the auto's to go a bit better, which it did.
Not sure that the injection pump is standard either - boost pin anyone?
The dyno results are somewhere, but, as we are currently living in a ******* caravan in our garden four YEARS into a TEN WEEK repair to our home, you'll be holding your breath for a while if you want me to post them. You would have to drive mine to know the difference..