Is this is a SuperJet B Chamber in an Yamaha FX-1? The Limited is longer than the Mod. Do you know which one it is?
http://www.x-h2o.com/threads/superjet-factory-b-pipe-on-an-fx1.41667/ This Thread says the Mod Chamber will fit? Maybe trade for a Mod Chamber?
Most of the B Chamber have internal braces in the Convergence Cone, right after the Belly (Mid-Section), but I've seen some that don't come with these internal braces.
If no bracing, then you can use a ball peen hammer and with many small hammer taps (peening) you can make the needed clearance. Any performance loss will be negligible.
But this denting will probably lower the resale value of the Chamber.