Good advice on this post! Another thing to keep in mind, modifications to the engine will void your warranty. Most dealers would consider pipes and high-flow air filters in this category, except perhaps if they sold you a customized bike. If you read the Tomos warranty, you'd conclude real performance mods will result in no support if other things break in your engine. And real performance mods put more strain on the clutches, engine bearings, etc. So, it would be a good idea to stick to the simple things until you've run out your warranty.
One thing I learned, the Tomos pipe actually works pretty well at eliminating the 2-cycle smoke (it has a catalyst), if you don't let it get fouled with oil. Unfortunately, a proper break-in doesn't really let the catalyst get hot enough to work. If you can borrow an old, stock pipe that isn't plugged and use it for the first 300 miles, your catalytic pipe will work, maybe for a long time, once you can run at full throttle. I liked the catalyst because, much to my surprise, no oil ever dripped out of the end of the pipe onto my garage floor.
I did the simple airbox mods. You might want to save the rubber snorkel tube to use as a sound-restricting air inlet. Some people drill holes in the far end of the airbox, but they let sound out, too. If you take a 7/8" hole saw and cut a hole in the far end, and then re-install that soft-rubber, 90-degree bend, to admit more air, it will help keep the noise level down. The stock airbox has a fairly small intake pipe which draws from a hole in the frame, so the frame helps contain the noise.
Beware of vibration. There are things you can do, so if you have it, ask and people will fill you in on that.