If I unplug my engine ECU to waterproof the connections, will I have problems when I plug it back in? I seem to remember reading something about having to get it re-coded to the vehicle..?

 

If you remove power from battery should not be an issue. I have even swapped one from a donor vehicle and have never darkened the dealer's door.

 

You only need the dealer if you install a ECU that does not match your alarm spider.
Do us a favor and do a write up on all of the water proofing will you? From removing the ECU, to opening it and putting it back.
Take lots of pics.

 

YES. Do it, por favor.

 

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