Fill in some of the recent history.
Did it used to start fine and then suddenly start having this issue?
You said you just bought a new pipe and silencer, was it OK before that and bad after?
Has it sat for a while since it was run last?
When you got it started, how did it run?
If the bike has been sitting for a long time then I would recommend draining the gas tank and trying with fresh gas.
If the problem started when you changed the pipe and silencer then I would suspect that the jetting requirements have changed with the new pipe. FMF generally provides jetting information along with the pipe so see what they recommend.
How long has it been since the top end was rebuilt? I would recommend doing a compression test and see if you have lost compression.
Rod