My again fuzzy recollection of the Djet is that there is a fuel cut circuit when you lift the throttle. I think there is a contact which closes when the throttle switch is going closed which operates that fuel cut circuit. I know you checked the operation of the throttle switch; but, the operation of that particular switch is something that you might want to give a second look at. I think it is supposed to go open just before total closure or at total closure. Maybe the sequence of operation for that contact is a little off.

Fuel cut on trailing throttle can be interesting on the B20E. I had my Megasquirt set up to radically cut fuel delivery when lifting the throttle. Made the car an absolute pain to drive smoothly. I think I have raised the fuel delivery on closing throttle to something like 70 - 80% which makes driving in heavy traffic a little nicer.

Using Megasquirt to replace the D jet isn't too bad if you are prepared to take the time to read through the official Megasquirt documentation and figure out how the thing works. It is definitely not plug and play and its best to avoid trying to transplant somebody else's solution. A lot of the web threads touting their MS implementations tend to gloss over the problems.