Drag Racing Tech - Wire cleanup in progress, got a question or two.

I'm stripping out a bunch of the misc stuff that will never get hooked up again, and have some questions for the guys that have already been there.
When taking wires back to the PCM, did you just cut the wire real short or did you pull the pin out of the PCM plug. If you pulled the pin, did you do anything to protect the plug from water or corrosion in the future? And if it went back to the firewall under the master cylinder, did you just cut it flush?
I'm not planning on stripping the interior so this round is just engine bay cleanup.

Thanks :)

If you just want to you can just put a small dab of silicone over the hole. As for me I'm not really going to worry about it as my PCM will be inside my car.

Going through it right now...im pulling all the stuff im not using at the pin. And i removed the whole body harness and have been building one of my own with just the essentials...i have not covered them up or anything on the computer though it should be alright.