I basically want it to be a track car, but is also open to being driven out on the road.
The only advantage of the Auto is using it to drive there, though since track events are normally over an hour away. But the reason I'm looking at Autos on M3's of all cars is because they are the cheapest M's available. Manual models go up to $15K & higher, but the mileage on them is higher than I'd like for my money. You may have missed it, but if I find a great car with decent mileage and a great price, I'm not going to back away because it's Auto.
In fact, I plan to keep this car to the point where I'd swap the transmission if it was an auto. When I want this to be a car I'll be keeping for a long time, I mean a long time.
Regarding 2 doors instead of 4-doors, I do realize the 2-door will be superior, but after watching videos of a DTM-tuned 4-door, I am confident I can still turn the 4-door into a fast car.
Once your comfortable, driving a manual is no hassle. Don't let the fact that you might be taking the occasional long trip turn you off from the idea. I wouldn't recommend a manual car to someone stuck in 2+ hours of bumper to bumper traffic every day, but long trips are no sweat. I really do think you'll eventually regret buying an automatic if you intend to make this a fun car.
I've got a friend with a 95 E36 M3. He found his in the 12-13K range and it was in great condition. 2 door, manual, and some dinan upgrades. I wouldn't "settle" for a car if I was in your shoes, I'd wait for the right one.