Yes you can swap ECUs just make sure that you get the one for auto. I believe that the traction control becomes inoperative when you switch to the OBDI but it TC sucks anyways.
I have a 97 6 speed and am running a 95 6 speed ECU. So far I have not had any problems yet. I have the Traction control ECU unplugged and am using a HKS trac-less kit to eliminate the restrictive extra traction control butterfly in the throttle body.
-pete
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