I just wrote a huge reply but erased it, damn.
OK, the problem you are having is the alternator going out. It might actually be the voltage regulator, but it is built in. The alternator is really easy to do once you've done it a couple times. I've changed mine 4 times and I can do it in 5 min.
The timing belt should be done every 60K. If it breaks you will just be stuck wherever it happens. Our 2.2's are not interference motors.
If you still have the adjustable shocks now is a good time to upgrade to something better. Tokicos would get my vote. They are stiffer than the stockers, and judging by your interest in the A4 they would be to your liking
Tokico blues run around $120 each.
With a turbo you have the best cheap mod avaliable. For $35 get a dawesdevice at http://www.dawesdevices.com
With the stock turbo you can run 12psi before hitting fuel cut. It will give you around 30 hp and ft lbs give or take. In other words, you will be smiling for a couple of hours afer trying it out.D
The biggest problem with this car is the lack of respect from Civic Si owners. After beating them you have to try and convince them that you don't have NOS, and answer about 300 questions. It is quite funny though! Otherwise the 2.2 is a very reliable motor. Mine has 170K. I had used 15psi for the last 35K or so with no problems, now I have a bigger turbo and 17psi! It hasn't exploded yet, but I'm going to build a backup motor soon.
Welcome to mx6.com and good luck with your car. There are lots of knowledgeable people on here. Between all of us we have probably done everything you can imagine to an MX-6. Just ask if you need to know something