To answer your questions (specifically, from a man who bought his first Ferrari - a 360 Spider F1
in April, 2013):
1. Red/Tan combinations seem to be the most popular. They are the easiest to picture, and probably immediately come to mind when someone says the F-word. No, not that F-word, the other F-word!
2. Transmission generally depends on your own comfort level. I can drive a standard gearbox proficiently, but I have driven F1 style gearboxes since 2002, so I am very comfortable with them. Plus, my wife canNOT drive a standard gearbox, and since I want to share the F-experience with her, I opted for an F1. The VAST MAJORITY of cars out there are F1 gearboxes.
3. The main differences within the model years are transmission control units, or TCUs. Early TCUs on coupes circa 1999 weren't the best. They got better and better as the years went by. Most people judge the ultimate TCU to be the one fitted to the Challenge Stradale - you can usually upgrade your car's TCU to whatever you like. My car is a 2001 Spider, and a previous owner had the 2004 TCU fitted.
4. I don't think your height will be much of an issue - it comes down to whether you personally prefer a coupe or a spider. I haven't had a convertible for about 7 years, so I got a spider, and I'll never look back. Your long distance comfort will be more affected by the type of seats (standard, Daytona, or "Race" style seats), how stiff the suspension happens to be over the kind of roads you drive, and the unfortunate lack of cruise control.
A 360 is a great starter Ferrari, but be prepared to pay to maintain it. They aren't "cheap" cars to operate, but if you can afford it, the process can be very rewarding. Good luck - PM me if you want more info / opinions. FWIW, I searched for about 1 year before Miss Right presented herself to me. I bought her within 1 week of her first listing on AutoTrader.