Yes Greg & Norm walk before you run, I've had several engines that were so tight that startup was a half day effort and they ran like arthritic, 3 legged dogs for the first 2 or three gallons of fuel...then they came alive & performed well. That's the point mods can be made and evaluated & I've no real problem with one at a time mods either Greg, but most mods don't show their real improvement until other tuning is done to maximize the addition of a particular performance part. I'd suggest reading the spark plug to begin with once you feel the engine "break in" and you know it's not going to improve past the point it's at & you then change fuel mix ratios (less oil to gas mix) & run about a half tank of the new mix ratio fuel through the engine...then read the plug again. If it's too lean or too rich, adjust. You may need a different size jet or a different heat range plug...perhaps a combination of both. It's a process.
When what you got, seems to be running the best it's going to get, is when you can efficiently start adding changes., but even then it's dicey and expensive if you're not certain where to begin & don't know exactly where you're ultimately heading. Study what experienced builders have done and ask questions along the way.
Your question: Yes port matching can improve both intake and exhaust flow. how much it helps depend on how bad these are restricted remember if the exhaust flange inlet of either the exhaust pipe is smaller than the engine jug port (quite common) that is also a restriction....as is a tiny carb air filter that blocks air flow. I've found changing to a high flow air filter from the one that comes with the NT kit carb has required a jet change up because it leaned the fuel mix out. So if you read the plug of your stock engine when it's first broke in and it seems rich simply changing to a high flow K&N style cart filter will bring the mixture back closer to the correct ratio, without a jet change. Again one small performance change either correcting a problem or causing a carb tuning problem that when corrected will make a bigger performance gain than initially experienced by just the addition of a less restrictive air cleaner. A good expansion pipe, motorcycle type, is another bolt on, kind'a, that can make a huge difference in performance, but can create a need for jet change up and or a carb upgrade to a Dellorto or Mikuni carb to furnish enough air flow mix. One example of a performance change that could require further tuning and or additional performance parts to maximize some or all the benefits possible from the exhaust upgrade. These are just basic changes that can build noticeable performance gains.
Lots more performance mods that require internal engine mods are proven to build hp/torque but each mod is enhanced, or should be, with the appropriate corresponding mods. If you don't consider what you've modified or changed along the way future performance mods can actually cut performance. Example piston port work, such as piston ramping and port timing on the intake side is no longer effective when, you convert to a reed port design, third port jug and piston "window" and without at least one of these two upgrades a reed valve addition can actually lessen power by as much as 100% 4 hp down to 2 hp...that's going in the wrong direction! An extreme example for sure, but I've seen it proven on a dyno.
If you are thinking there are performance gains to be realized with these small engines you are correct, and it's a fun process that usually takes time and some insight/experience/experimenting & $$ along the way.
Don't get discouraged by the process, lots of great running high performance 2 strokes on this forum and yours can be one of them!
Have fun.
Rick C.