I have had similar problems where the reference pick-up (once every 360 deg)on the flywheel has fallen off but it scopes the hole left by the missing peg! What is the voltage of the peak on this reading or can you post the pattern?
The pick can also be faulty by not giving out the correct voltage.Has anybody swapped over the crank sensor wires as I think this was possible on the early models.You could test the sensors by swapping them over and seeing if the signal strength changes.(they may require jumper leads if different plugs)
On the 2 plugs with 35 pins do you mean 70 pins?? You could have the wrong control unit (but I do not know what)Do you have the number off the ECU and normally it has Motronic written on it to help you!!