replacing CD player in 96-98 Civic

Hey all,

I have a 97 Civic with a factory CD player, which is mounted down by the cup holders. I was thinking of getting an aftermarket stereo, but I read that the stock stereo (the main part) controls the keyless entry and some other things. So I was thinking I could put an aftermarket deck in the space where the CD player is now, but it doesn't look like there is enough depth for an entire deck. Plus floor vent is directly behind the back of this compartment, which might make for easy overheating here in MN. Has anyone ever tried this?

Thanks in advance