Can you source a manual ECU for your model year? That may be the difference. Maybe find someone who is willing to let you plug theirs in briefly to make sure that it will solve the problem and then source a manual ECU on your own.
As for tricking the ECU, if you knew what it was looking for from the TCU (+12v, wave form, ground) that would help. Could you wire the TCU in temporarily in order to find out?