I run straight through exhaust on two of my bikes and yes it is louder but as long as the carb is tuned for the extra air flow it wont hurt a thing.
If while under throttle at cruise speed it does what is called 4 stroking In stead of a smooth buzz like what a weed wacker doea when its revved up that means its running a little rich, doing what is called a plug chop or as I call it check spark plug color you can determine when your tune is right, its better to be a little on the rich side than to run an engine lean, these engine will 4 stroke. Some making that blubbering sound at low rpm with no load or little on them but then under throttle they should clean up in sound to a nice 2 stroke brayyyyyyyyyyyyy sound, I dont change jets in my NT carbs I just solder them up and redrill them with a #72 or #73 wire gauge drill bit the bits can be got at widgetsupply.com and a set is about $5
This is the most inexpensive way to change jet size and all it takes is a dab of solder and a small propane torch to heat the jet enough so that the solder will melt to it and fill the hole and it only takes a very small piece of solder to do it.
Hope this helps some and you get it running great soon.