that code is for the INPUT speed sensor not the VSS/OSS. its pretty rare that an ISS has failed, more likely there is a wiring issue...i know you swapped the motor and/or trans, make sure the harness isnt stretched, or chaffing somewhere. also make sure the trans main connector is plugged in all the way. i cant explain the loss of boost but everything else fits.
maybe the BBV is engaging a little because it the trans adapts and whatnot are defaulted?
id get an ohm meter and check the wiring and then you'll need to ohm out of the ISS via the trans connector