Its a good idea to rebuild the bottom end if you really messed up the top end. Gotta get all those little chunks out as said above.
If you don't have any deep scratches,gouges, or chips taken out of the cylinder wall, and aren't at your maximum bore (66.50mm) you will be able to bore your current cylinders without resleeving. Best bet would be send the jugs out to a site sponsor like fast, hjr, or wildcard and get it bored and buy all your parts from them.
Porting is done by a builder. It is your best bang for your buck. If you are riding a stock engine and want more power I would get it ported. A builder can port a motor to perform however you prefer. Lots of top end/mid range/low end.
Even if you buy an athena or cub kit, ideally you would still want to spend the money to get it ported to your specific tastes.
Yes, you can just get your top end ported with no modification to your bottom end or crank.
If I was you I wouldnt spend the money on new cylinders, if you can get away with it, and get your top end built by a sponsor. Then you can also use the money you saved from the big bore cylinders and spend it on the bottom end. Might as well do it right from the get go and you won't have to worry.
Get in touch with a site sponsor and they can really steer you in the right direction.