Jim this is a little late
but I would have set the motor further back and either trimed a little off the breather or made a basket for the breather (small wire jewlery or notion box works great form to fit add foam) that would have given you room for the muffler one thing I have not seen is as the motor breaks in you will have a little oil drip out of the muffler inbetween cleanings of the muffler and I would be afraid of what a back wash of dirty oil would do to the motor.
As for the breaks you may have to re adjust the ones that came on the bike any bike shop can show you how to do that or get a bigger break .
This is a littke
FYI if you have a lpace in town that installs garage door openers go talk to them about their old chains they are very long but the tooth size is the same as what we use on these motors and they also have the lock keys ......on my first bike I could not adjust the chain so I went to one of those places and they adjusted the chain and gave me a hand full of the keys and several long chains that they where going to throw away.