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I know for my old Mitsu they could. The TCM signal wire just had to be cut. For some reason Autozone lists the ATX at a higher price than an MTX ECU (even though the ATX is technically more complex). Wierd
I personally wouldn't use an auto computer in a manual in an OBD2 vehicle, too much stuff to mess with. Of course you could use something like SCT to remove the tranny stuff from the computer.
In my manual OBD1 truck I'm using an auto computer without a problem though.
oh ok the one thing i didnt think of was a manual or automatic..... lol im not sure what year obd2 started? would i be able to keep the automatic computer in my 97 dodge neon if i swapped in a manual?