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if i get a bp motor from an automatic protege, as long as i swap MY flywheel and clutch itll work on my 5 speed right?

and one more thing, i read that the ecu for auto's are diff then the 5 speed ecu's.. is this right? would an engine that came off an auto car work with a 5 speed ecu? or would it be messed up? this would be using the sohc harness thats on my 92... and atm my car is a 5 speed

Neutral safety switch must be bypassed for the AT ecu to work in the MT car.

It has been done before.

Oh and the AT BP has a 4 wire TPS where as your MT MX3 and the MT BP have a 3 wire I believe.

I have a 1990 Mazda which used to have a 1.6 SOHC 5 spd and now it has a 1.8 DOHC. I have a BP10 (AUTO ECU) and I did not do any bypass for safety whatever you are talking about.

The only difference from Auto to 5 SPD ECU is Automatic signal, the 5 spd does not read it or in other words is useless signal, but if the car is auto it needs an auto tranny.

The engines origin, be it from an auto or 5 spd does not matter; both will work.

If you use to have a SOHC you need an extra cable from the DOHC distributor signal to ECU and from the VICS solenoid.

Be sure to use the ECU from the car your new engine is from, otherwise the engine will not run at it's full potential (if at all). One thing to note is the differences between manual and automatic transmission cars. The TPS is different between these cars and will not interchange. 5-speed cars have a 2-plug ECU while Automatic transmission cars have a 3-plug ECU. Interchanging these ECU's will require serious splicing, so be sure to get the proper ECU for your car. It is also easier to get an engine from a car of the same style transmission to avoid the TPS interchangability problem.

above is copied from the swap FAQ written by Gro Harlem.

I'd be willing to bet that your BP10 ECU was from a MT car, b/c if it was from an auto, you would have had a bunch of wiring issues as Will wrote about above.