Well I recently bought a used '99 Honda Accord EX sedan. It is in pretty good shape. It has the stock Matsu****a double din single CD player in it. and the upgraded six speaker factory system with tweeters on the dash. 6.5" in the doors and 6X9's in the rear deck. I noticed when driving that the stereo did not sound as good as it should. I started poking around the car and found a monster cable with NO inline fuse attached to teh pos side of battery and CUT under the pass seat!!! They drilled a hole way to big in teh fire wall to bring it through. After seeing that I pulled the head unit out and got sparks from twisted and untaped wires where a a LOC had been spliced into the FACTORY wiring harness! The RCA wires were still connected and were cut under the dash! What is my best bet to fix the $&%*^%*& hack job. It blew the fuse to the radio when the wires shorted. he only cut the factory harness going to the rear speakers. My guess is he had a gehto sub in it with teh factory set-up.
I hate hack jobs but we get a few in our shop. There is no quick fix. Basically you start at one point and start fixing things. The way I would tackle this, is to rip everything out and start over. As far as the hole (hopefully its round) you should be able to find a Grommet. I know we keep grommets in our shop for up to 1-inch (yes thats 1-inch) holes Good luck and take your time.
I'd just cut a round piece of sheet metal and weld it on there if the hole is massively big lol...why?? cuz I'm a welder whoo hoo