Originally Posted by dropnosky

yeah, but I think he's saying that the absence of the automatic tranny in the car built with the automatic tranny will create a hole in the interwoven ECU system on the recipient car.

In other words, the manual tranny will certainly work, but there might be some issues with MIL lights, or even perhaps some drivability issues if the ECM is looking for calculation data from a tranny that is no longer there.