Those bolt bosses...run them down flat so they're flush.

And the two bolts that go into those spots...cut them so they're flush as well.

As for the silencer ports, you can open them up a little bit as well. I've seen that done as well...this was my Green Bastard blower that was done in and out, quite a bit of porting was done to it. I'll have to dig up a picture somewhere.

https://www.youtube.com/watch?v=8S7v4HZF11E