Unless you own a 5spd.... I'll elaborate.
Theres an obdII connector in the 5spd. What difference exist between the 5spd and auto ecu's, I do not know.
Some obdII readers can read the trouble codes on the 5spd, but freeze frame reads of sensor data is broken. I can connect freediag (obdII computer software) to my '95 legacy auto, but not to my 95 legacy 5spd.
My auto has an egr valve and backpressure transducer, but the 5spd does not. Where the egr valve would be is a plug. Ignition timing also is different between the two engines (beyond learned ecu behavior).
If you're going to transplant the engine, i'd put an auto trans engine in an auto and vice versa. I'm guessing you'll want to switch over the ecu too.