Keep your fenders and try to find a stock airbox. A seat is gonna be hard to find given your frame geometry and the stock one actually looks pretty decent all things considered. Get yourself a factory Honda manual in for free online in PDF, print that sucker out, bind it, and go through the FULL tune up procedure in order. Go ahead and clean the carbs thoroughly first. If the exhaust is still making weird noises after that, you might pull the exhaust and see if maybe the baffle is loose and rattling around, it can happen. A set of Progressive springs in the front and rear can make a world of difference. Otherwisse, if it ain't broke don't fix it.
Edit: the easiest thing to change out that will make the bike look sleeker and sound a bit meaner is to fit a set of aftermarket mufflers. If you are going to do this, I would do it first and then go through the tuning procedure. Another easy way to clean up the look is to loose the big bulky taillight for something smaller and cleaner. Lowbrow Customs and Dime City Cycles have a great selection of universal parts.