The R3 guys will ether tell you the R3 handles just as well or better than the Tbird. But the fact s thats just not true. Most never rode a Tbird and just assume the R3 handles better. they are a VERY prideful bunch. Truth is the R3 doesn't handle near as well and the reviews and user comments support that. I found the R3 to be quite a handful and thats one of the reasons i didn't care for it. It's a FAR bigger bike regardless of the fact theres not a hug weight difference. theres a pic somewhere here of the R3 parked next to a Tbird and the thing dwarfs it by what looks like 1/3 more size. It's much taller too, so the COG is w/o a doubt higher, and it surely felt like it. The R3 may however have more ground clearance as a side benefit. But thats not much consolation if it doesn't handle as well to begin with. And to tell you the truth i've come to appreciate the Tbird's peg clearance because it keeps me from taking too much advantage of the handling. I can take corners much faster than i should as it stands, and the pegs keep me from pushing it into the danger zone....well, the UBER danger zone. Maintenance costs I can't tell you beyond the obvious. But one obvious thing, higher tire costs and less mileage from tires alone scares me away.
The tranny issue you mentioned has been fairly common as have some other issues equally distressing. Again, another reason i shied away. The reliability issue was probably the main reason i passed. The Tbird was only a rumor then so the R3 was my only option for more power if i wished to stay with triumph, which i did. But i saw so many posts by people posting about thier major engine problems with them i would have passed on that point alone even if i loved the bike. Now i have a bike i feel is far better in every way for me except power, and with the 1700 kit and tors i really don't pine for power like i did with the speedy. So all i can tell you is how I feel, and thats how i do. But who knows....you may feel different. The fact you are considering it tells me you aren't happy with the Tbird, so it may be worth it to you. I personally cannot imagine giving up all else for more power, especially when i have more than most bikes in my Tbird.