OP, kscarrol has already provided some great feedback to your questions. While I don't own an M3, I have recently placed an order and had similar questions.
On not having a spare tire, yes it is a slight concern but you do receive the M-mobility kit. Short of the tire self-destructing, this should be good enough to get you to a service center. There might be vendors who offer a space saving spare. You may want to check with some of the forum sponsors.
End of Production, currently is scheduled for June 2013 for the coupes (E92). That date can change and most likely to an earlier time. Dealers don't know how the allocations are going to be in the closing months. If you are intent on buying an M3, start working with a dealer now.
MT vs. DCT, both are good for different reasons and there are people passionate about one or the other. There's no right answer other than what is best for you. My recommendation, find a local dealer with a DCT equipped M3 and go for a test drive.
On the carbon fiber roof, this is the unique feature of the M3 coupe. Sure there's a weight savings and reduction of the center of gravity. As compared to a coupe with the moon roof, will you notice a difference, most likely not. It is a nice contrast with some of the exterior paints (including white, silver, red and blue). On a black vehicle, IMO, it just blends in. Would you use the moon roof? If not, go with carbon fiber.
Just go through your options list carefully and if ED or PCD pick-up, work with one of the forum sponsors. They can be found in the "Ask a Dealer" area.