I just got a 1999 gs400, and the first thing I'm thinking about is the stereo upgrade.

I have the navigation with ML

I was looking at 2 different routes

1) replacing the stock subwoofer with a 10" piece. Will I have to get a new amp? Anyone have pros and cons? I have heard this setup on a 93 gs300, it sounded horrible, maybe it was his setup.

Or

2) getting a box to put in the trunk. I already have a 12" JL and phoenix gold 500 watt amp. Is it hard to rewire it? I have read about taking out the stock 10" and linking it to the aftermarket box.

Any help or suggestions is appreciated. Pics would help too.

 

Either direction should be pretty easy, I would go with the second route though. The bass would be substantially deeper and louder. If you go with the freeair route, the bass will be more natural but overall output would be less.

Either way You will need to add an external amp.
You could tap into the factory sub speaker wire and convert it into RCA outputs with a high-to-low converter.
Other then that, just run your power, remote (tap into the ignition switch on the steering column) wires and ground your amp and you're set.

This post should help you out.