Replacing the NAV on a 99 will not impact any other electronics and will work with your amp and speakers. The easiest bet would be to replace your stock unit with a double din aftermarket unit. If you pry the horseshoe trim (upside down U trim) above your radio that stores all of the switches, you will see the sides of the nav with two tabs that need to be pushed in to unlock the unit which will allow it to slide out.
You can pick up a double din face plate mounting kit and replacement cubby hole for your nav so it looks factory. Do a search on google for replacing the stereo on a 99 996 and you will get some hits with technical details. I just replaced mine last week but included new speakers and amps - sounds incredible.
You may also want to contact Car Audio Innovations or do a search for them on the 911 forum - they work on Porsches and have pretty good solutions.