Hopefully someone can back me up on this info as I've not done a swap yet.
I believe it is not necessary to swap ECU's in order to having a working 5 spd. swap.
However, it is very easy to swap ECU's. You should find the ECU in the right side of the passenger footwell. Just past the door behind a plastic panel. The ECU may be held in place by a couple small brackets that you can unscrew. To replace the ECU it's as easy as removing the wiring harness and plugging it into the new ECU. The harness connector is big since there are a lot of wires, so it usually has a allen head screw to fasten and tighten the connector into the ECU.
Too my knowledge, you may only need the wiring for the manual transmission alone. The rest of the engine and body harness are just fine. I am sure you can create new wires for the lower harness if you need to.
Check out this thread/article for more info.
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