That wouldnt explain the harsh shifts so much - the Auto Trans Controller should work fine - but youd need to trick the ECU into thinking it had an auto attached to it....

.. or change the auto wiring so that it did.

would an eaII ecu and manual loom work in an ebII without changing anything? btw the ea is mpfi and so is the eb would i still have to put resistors in and cut the loom or just plug and play?