where to start...
You should put lot of thought before hand in knowing what you would like out of your engine.
A standard engine has had lots of care in finding the right balance between performance, reliabilty and fuel consumption and changing any of this variables even slightly can in extreem cases result in more expenses and lots of time right in the drain.
If you'd like to go for a standard cylinder you may find the right compromise between performance and cost in a Simonini exhaust. It improves high rpm taking somewhat little away at lower rpm but a 200 has backets full of torque and you'll hardly be able to tell, it has a higher pitch and it will probably give you around 5 miles extra on the clock, if you'd like to go for it make sure to fine tune the air/fuel mix changing the max jet with a slightly bigger one. The standard get you have fitted should be 116, I reccommend you you try a 120 to start with and maybe decrease it to 118 if necessary.
I have also tried sito and polini but was not at all impressed with them.
The cylinders topic. Lots to say, lots of different ideas on that.
There are 3 main choiches in that respect: Pinasco, Malossi, Polini.
Pinasco is the most expensive, it's kit comes complete with a head, it's the most reliable being alluminium cast, it can be fitted plug and play but will not give you great performance improvement.
Malossi is the middle range, it comes without head, also alluminium but needs working on the cases ports. I have never tried it but was told it gives at high rpm
Polini is the cheapest, the rudest, the richest in torque, the most delicate, it also comes without head and needs lots of care as well as ports adapted. It's my love but lots of people utterly dislike it due to its "easy seaze", mine lasted much longer then the Vespa it was fitted on (I was told my case is probably unique). It's now waiting for a set of cases to be put on.
To answer your question about polishing transfer ports, if you go for the standard cylinder I find it to be useless, just keep them as they are.
Hope this helps
Emilio