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Hey, Saff -
3B's have the fully synchro transmission and the larger displacement (same block, though) engine than the 3A.
Mickey
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Actually, the 2.2l engine came out mid-year in 1959 as an option. One could still order a 2.0L engine throughout the rest of the 3A production, as to enable racers to continue to compete in the SCCA's under 2.0l class.
In actuality, the 2.0 and 2.2 offered almost identical performance. The 2.2 was a little torquier. It is pretty much impossible to tell a 2.0 car from a 2.2 car without pulling the head and looking at the liners (or testing Bonneville Salt Flat style with putting in fluid through the spark plug hole and measuring it!) So many engines which were originally 2.0L have been relined with 2.2 liners (because that's the only difference, the size of the liner that drops into the cylinder--and the piston/ring.)
Interior colors on the 3Bs were limited, and there's a long-running debate on which colors were available. Some have said "only gray," while others claim "just gray and black."
The largest difference between a 3A and a 3B is the all-synchro gearbox, although there's nothing preventing an all-synchro box from being put into a 3A (and many have done this.)
The big issue to consider in a 2 or 3: Early parts are often not reproduced, and things as simple as a thermostat for an early TR2 (bellows type) can run big $$$ (I think the Roadster Factory just found a bunch and are selling for something like $80 each!)
Also, the TR2 and TR3 (small mouth) tended to overheat, which is why they went to the larger opening in the TR3A (which is still called a TR3 by the factory, by the way.) If you're in colder weather, it's not an issue. In warmer weather, it should be a consideration.
Another consideration: In late 1959, the tooling was changed, as were the bodies. A real package shelf replaced the cutouts behind the seats. It took out about 4 inches of potential legroom, but made it easier to carry items on a flat surface. Since you have a GT6, I'm guessing leg and headroom aren't a big issue. For me, however, I went from an early '59 TR3A to a late '60, and the change was definitely noticeable to my long legs.
Other minor things: The later 3As and 3Bs have a rheostat for dimming the gauge lights, and more importantly, they have smaller rear brake drums, which might seem to be a bad thing, but in actuality, it solved an issue with the rear brakes locking under hard stops.
I'm sure there are other things, but I'm going off memory here!