[gatos]

I am not ruling out the ECU, but I have never heard of a similar problem being caused by the ECU.

I am trying to backtrack what would need removing from your car when replacing the clutch.

The crankshaft position sensor would have been disconnected, EGR connector, dump valve connector at the back of the inlet manifold, MAP and MAF sensors. Have you made sure that all of them are undamaged and plugged in properly?