RE: Any downfalls for riding without muffler?
 

It should be lean if you remove the pipe, the restriction to the exhaust system, it will allow more air to flow through the fuel system and make it run lean.
Installing the PC on your FI bike is like jetting the carbureted ones.

RE: Any downfalls for riding without muffler?
 

Can you replace the cannister with a slipon streight pipe and a baffle? Would that give you enough back pressure and prevent you from running too lean?