Generally speaking I'm pretty happy with the factory bose system in my S4 although shortly after getting the car I did add an Boston Acoustics ProSeries 8.5LF 8" subwoofer to improve the bottom end; it does an excellent job. Details here. I figured if I was happy with the system that adding good clean power would be an improvement. I began a project to swap out the bose amp. I had no intentions of replacing speakers or the head unit.
I purchased a Alpine MRV-F357 (5-channel amp) and I already had an MRV-T501 2-channel amp bridged running my sub. My plan was 7 channels of power: 2 front doors, 2 rear doors, 2 rear deck and the 8" sub I already had. The catch to the whole project was I wanted to use the existing wiring but I didn't want to hack up the factory wiring harness to hook everything up. I found connectors at a local electronic surplus supply (no, not RadioSnack) that allowed me to build a harness that plugged into the factory connector which I could then hook up to the amps. The harness took a couple hours to build but the final result was a clean, non-destructive way to hook everything up. I'm sure the electronics guys are wincing at this setup... but hey, it worked for me. : )
The HarnessWhile assembling the harness I swear I checked the pinout 10 times. Anal? No, I just don't trust myself. After it was done I checked it again. Wire dyslexia... an aliment I suffer all to often. Check those wires, it's cheap insurance to prevent smoking electronic components. Once complete, you simply unplug the harness from the bose amp, plug in your spiffy new custom harness and connect everything to the amps. The connectors I used for the harness were not easy to find--apparently the spacing on the factory connector is a bit odd but I found some connectors that did the trick at a local electronics surplus store. With my setup I used 2 connectors that plugged in side-by-side which I then secured with tie straps. I was unable to find one that would plug right in (gee, what a surprise). Sorry, I will not be providing step-by-step instructions for the harness. If you don't understand what to do with the pinout information below I'd suggest you have an installer do it for you. I'm comfortable doing wiring on my own car but not someone else's. Also, I strongly suggest you check your car carefully before doing anything... ya never know when Audi is going to change the pinout!!
Good Work, Bad Sound
Good plan, good project but all for naught. I plugged/hooked everything up, checked my wiring and fired up a CD. Music starts to play... hmmm, this doesn't sound very good. I know I checked the everything many times over but something was just not right. After some digging, listening and testing I determined that despite that my wiring was correct the front speakers and rear deck speakers were out of phase with the rear door speakers. Looks like Bose runs the front speakers out of phase with the rear doors to spread the sound stage around the cabin and the rear deck speakers out of phase with the rear door speakers; probably an bass timing adjustment. (The sub in my house is out of phase with my mains due to acoustics so this didn't surprise me.) But, even after getting all the phase issues sorted out the system still sounded like errr, uhhh, well... total shit. I spent a total of 8 hours fiddling with levels, balance, phase, everything. Sound = Total Crapola.
Bottom line: it appears you need the EQ adjustments built into the bose amp for it to sound right with the stock speakers. If you want to upgrade the system you've gotta replace the speakers too. Please, no flames about how I should have known better. In the past I've upgraded non-bose systems with just better amps and had very positive results.
It's Outa There
So, believe it or not, I took out the whole works out of the car. Thanks to my harness it took me all of 15 minutes to put the system back to my original stock + 8" sub setup. Time and labor I'll never get back... oh well. Stock bose + sub, it's not aftermarket high quality sound but it works for me. I'm a home audio nut and I've given up on trying to get superb sound in the car. If I want stunning tunes I park my butt in the living room.