I think Gcalo's advice is generally sound although I see a few small things differently.
Even as a life-long 3-peddle guy, I found the 360 F1 transmission to be superb. It's astonishing smoothness and effortless precision must really be experienced to be appreciated. I find the F1 much better on the street than 3 peddles, especially in heavy traffic where lots of shifting is needed. It's true the F1 was developed for racing and is clearly superior there (meaning faster around the track) but it also saves a lot of left leg action in heavy traffic. The notion that 6-speed clutches last longer than F1 clutches is really a matter of proper adjustment and driving style. Clutch wear in a properly driven F1 has proven to be the same as a properly driven 6-speed. Any knowledgeable driver who gets good mileage from his manual Ferrari (or Porsche) clutches can easily get the same high mileage from his 360 F1 clutch.
There is no doubt the F1 is more complex than a 6-speed and can (emphasize *can*) be more expensive, especially if routine maintenance is neglected. Also, clutch replacement is certainly trickier and should only be done by a well trained and experienced technician using the factory SD/2 or SD/3 (now actually SD/4) computer for proper installation and adjustment. Improper adjustment is the other big factor (besides driving style) which affects F1 clutch life so plan on factory trained maintenance only for your F1.
I believe DIY for routine maintenance on your 360 is fine but "by the book" is especially important because of the many subtleties used to achieve the outlandish performance of a car like the 360. A special torque wrench just to screw on a silly oil filter mentioned by Gcalo above is a good example. An example of how serious it can be is the guy who installed a clutch in his 360 6-speed (F1 clutch DIY is really not an option) which resulted in total engine meltdown 3 weeks later. Even though he thought he was only working on the clutch, he unwittingly introduced blockage of main engine oil circulation to the bottom of the front two cylinders. Since it's a dry sump engine, both rod bearings and crank journal were toasted resulting in valve crash resulting in bent heads, etc., etc.
I agree all 360s can (emphasize *can*) be equal, but there are some model year issues to watch for. Several very serious problems were discovered in early models which were corrected by subsequent factory "campaigns", and there were a couple very nice upgrades in later models too. Starting with MY'02 everything was fixed and upgraded from the factory so the trick is insuring *all* campaigns have really *really* been done if you're looking at a '99 to '01 car. It's not difficult to be sure an earlier car has all campaigns and/or upgrades installed, but extra due diligence is definitely required for them.
By the way, my 360 has been fantastic -- the more I drive it the better it runs. Dead nuts reliable and what a hoot to drive. Best of luck!
"Fear of guns is a sure sign of retarded sexual and emotional maturity." -- Sigmund Freud, General Introduction to Psychoanalysis, 1906.