Triumph can put you there tune in for cat delete and off road pipes.Did this on mine when i removed the cat but kept the standard pipes.It shouldnt be running rough though.
Did you toss any papers or anythign under the seat, I once almost crapped myself when my bike kept choking out, then realized my DMV papers under the seat were sliding over the stock airbox. and cutting off the air...
With the Staintunes you need to have the dealer load the aftermarket pipes tune. I have the same setup with the additiona of a Uni air filter. Runs great, no problems.
Start reading the threads about Tune Boy. I can't just tell you to spend the money as it isn't a simple bolt on fix, but someday you will be getting one. IMHO the sooner the better.