For a complete write-up and very good reasons as to why you should get a manual engine and ecu can be found at ORS's website- specifically by clicking HERE .
For the extremely lazy here's the excerpt you're looking for taken directly from the aforementioned page <img src="/forums/images/graemlins/wink.gif" alt="" />
"If you are using a manual transmission, the 3.4L engine needs to come from a manual transmission vehicle. In SELECT year models we have found a difference in crankshaft machining from the factory. In these instances an engine from an automatic transmission application will not accept a pilot bearing. Another reason to purchase a manual transmission "package" is the difference in electronics. The engine ECU and the engine wiring harness are completely different manual to auto. Based off experience, we recommend purchasing all the used parts from the same manual transmission vehicle. Once again, purchasing all used parts from the same donor vehicle has been proven to prevent grouchy mood swings." ~ORS
HTH,

~R

94 4Runner 3.slow-5spd, 4" coils, 1.5" BJ spacers, 2" BL, 35x12.50 Nitto's, 5.29's with a front Lockrite and a rear Detroit; 250k miles and lots of offroad time...and by offroad I mean on jackstands.