You should be able to get the car ~3200lbs fairly easily. Starting with a base M3, take out the M mobility kit, add light weight 18s, light weight exhaust, light weight battery, seats and a few other odds and ends and you should be well on your way.
Also if a good track car is what your looking for don't forget the Lotus Elise will be here soon, a almost "nothing extra" car. Its the best handling car in the world with the power to weight of the M3 and ~8000 less than the M3 you are looking at.
As for the SMG, I am a dyed in the wool clutch pedal guy and have a non-SMG car BUT if my primary focus for the car was track the SMG would be a no-brainer. There is few things more satisfying than a well executed heel/toe shift well except maybe lower lap times, which unless ones name is Boris Said or Hans Stuck the SMG is likely will result in just that. Having driven a SMG on the track I can say I was immediately faster, that said I still chose the manual clutch car for a daily driver. The SMG weight penalty is ~17lbs.
For the M3 at the track I would suggest above the weight saving bits, in no particular order:
1. PSS9s
2. SSK and Redline if no SMG
3. light weight 18's with 265s all around to balance the understeer
4. 4/5 point harnesses
5. sways
6. 4.10 rear end gear
7. brakes (minimum pads and fluid as a minimum, if cash isn't an option then Brembo BBK) M3 brakes are GREAT for the street but is probably the greatest limiting factor on most road courses)
I personally wouldn't bother with engine mods until I had done all of the above, the S54 doesn't tune cheap or easy and the dyno numbers are less than impressive!
Vandy