Not sure if you found the cause of your vibrations but, for what it's worth, I had a problem with vibes between approx. 3200 and 3800 RPM, regardless of gear. My local Trumpet tech said that, to pass emissions, Triumph (and all vehicle manufacturers) have to lean the fuel mixture out at a certain rev range (less fuel=less emissions); the rev range they test at is between 3 and 4k. Your aftermarket pipes (I have TORs) accentuate this leaning out, causing more noticeable vibrations.
Go for a ride and you should see that the vibes are more apparent between 3 and 4k revs, rather than a set speed. (If not, then it needs investigating)
(Note: if you look at a dyno reading of any production vehicle engine, you'll notice a dip at approx. 3500 RPM. The idea of tuning/dyno-ing, etc is to reduce this dip as much as possible.
neill
