Repairing and Installing Intake area?

A little bit of back story here to get to my main issue, I got my celica a couple years ago from a guy who once took it to a shop of questionable skill and trustworthiness to have a cold air installed.

I think the brand is AEM but the pipe isn't branded, its metal and gunmetal gray, I still have it and want to reinstall it but the shop cut part of the weather guard out from under the car down below the Fender where the Intake should sit because the filter was too long or something. Well of course when you put your Intake below your actual car it sucked up water and blew the engine. On the upside when i bought it there was a new engine, with a stock Intake, but the hole remains in the plastics.

Anyway originally I thought that I would just patch the plastics with new ones, or get an Intake box to put it in down in the Fender area. Then I thought if I just cut a few inches off the pipe it wouldn't affect any of my sensors or other hoses, the Intake would still be down in the Fender, and it SHOULD be far away from any moisture when driving in the rain since its a daily driver and it will happen. I figured I would get some others input on it since I'd like very much to not do something stupid and lock it up. My biggest concern is that even if i patch the plastics under the car the Intake will still sit just behind the fog light and since I drive my car A LOT i dont want to risk having some splash up from someone in front either.

Any input on this? I've had vehicles with cold air Intakes on them but never actually installed a true one. Want to make sure it gets done right.

Your car may win show trophies, but mine earns battle scars.