You may have solved the problem by now, but I experienced the same EGT indication with our Aeroprakt A-32 when the Carbmate synchronization tool was connected. At prolonged Idle the CHT on cylinder no. 1 went below 300 degrees F, while the others were between 400-450 degrees. The temperatures were normal at higher rpm, and the problem dissapeared when the synchronization tool was disconnenected and the balance tube connected again. A fellow club member said that this was normal behaviour with the Carbmate. I don´t understand the reason behind this though.
Now, I understand that this is happening to you without the carbmate, but could it be that some of your new instrumentation introduces a small leak or disturbance in your fuel/air system?