Who's the dealer?
If it's the one in Nerang, speak to Welshrob, the mod on the Speed Triple Forum. He's the Ratpack leader and should be able to get the dealer to do the right thing.
Sounds like you need to get them to do the right thing.
1) Adjust the clutch via the book.
2) Check the plugs and the coil connections - no water pooling in the plug sockets?
3) check the battery terminals are tight and clean
4) check the wiring harness for the ignition
5) re-install the aftermarket pipe tune.
Don't let them tell you it's all an un-documented feature!
Mick