RE:What materials would I use if I just made a window?
What do you plan to do, aim the remote BACK at the console and relearn the buttons ??

You're going to HAVE to deal with a receiver and an emitter. If you find someone froggy enough to go inside the head unit.... RUN AWAY from that person.
The good news is that almost every IR repeating system has a DC power supply. Some run on 9Vdc and some on 12Vdc. You should correspond with a manufacturer or two and once you decide to take the plunge, experiment with functionality BEFORE you take the Sawzall to your dashboard.

You could put the IR receiver back a little ways under your dash on an "L" bracket of your own design and run the wiring down under the carpet along the trans-tunnel and inside your console to the emitter. The connecting blocks are designed for multi-component functionality so you'll most likely have to live with unused emitter jacks.

I saw this done with a Kenwood unit that CAME with a little IR remote receiver. (Build of this head unit was sub-standard by my standards.) The receiver was mounted under the dash by the passenger's kick panel so the driver could just lazily aim the remote like a sawed-off shotgun and hit something every time.

I'm sure this is happening on a daily basis in the Car Audio world but I've been AWOL. Go to a Car Stereo forum and repost this there.

Wait !! Go to a dealer who's got the same head unit in his display. Take along a little self adhesive convex mirror (about 2" dia.) and a decent sized piece of the mystery tinted lexan or plexiglass you intend to use. Have a helper hold the lexan (??) over the IR pickup window on the head unit. Position the mirror out about 3 & 1/2 feet from the head unit and while holding the remote up close to the head unit point the remote away from the head unit towards the mirror. Try skewing the plexi (??) AND the mirror in different combinations to see if you can make it fail, and if so how hard do you have to try. If you get reliable IR commands to your head unit saw your hole, mount your tinted "lense", and mount your mirror under the dash (on an "L" bracket of your own design?) If you've got an open Jeep you may be able to stick the mirror directly on the interior side of your firewall.