Actually taking out the rear speaker will help in sound quality. 99% of serious sound quality installs run absolutely no rear speakers.
If you have a good front speaker system with adequate power from an external amplifier, then there is no need for rear speakers, and in most cases can throw off the imaging and staging that a well installed and tuned front speaker system produces.
Check out the new EU-700 from
www.edesignaudio.com
It should fit into the stock opening and will work very well as a free-air sub. Just gotta check the mounting depth limit in the stock rear speaker opening.
Also factor in you should be using a MDF baffle to install them, so that will give you anywhere from 1/2" to 1" of extra mounting depth clearance.