I had a difficult time sealing the intake manifold boots on my '03. The standard clamps just made the job difficult. I solved the problem with aftermarket intake clamps from BellaCorse...
http://bellacorse.com/shop/parts-for-triumph/engine/stainless-steel-intake-manifold-clamps/Also, going with Thruxton needles, fattening up the idle mixture, and selecting the right main jets will transform the engine's behavior. You'll lose just a little gas mileage, but the response is far more linear...