there are a million threads on this. however i have some answers for your simple questions:
when you're talking about raising or lowering, you have to imagine that your cylinder is vertical, like it is on most motorcycles. raising a port means making it open further towards the cylinder head, lowering a port means opening it up further towards the engine. widening a port is....pretty self-explanatory.
mess with the ports, raise them, lower them, widen them, but research what to do first, the first time i ported a stock jug i just blindly made all the ports HUGE thinking thats all it took, but no. port timing is more of an exact science than it seems. basically what i ended up making was a cylinder with insanely wide ports, with way too low an intake port and way too high of an exhaust port. needless to say, the bike RAN, but it didnt go anywhere.
you have to do it decimeter by decimeter. check any threads with port maps to get a good idea of what other people have found to work best, or once you really know the science behind it, experiment and get the cylinder to do what you want it to do.
if you only have ONE cylinder, i wouldnt recommend this. however if youre like me and have crate full of puch top ends, go crazy.
oh, and to do the porting, depending on how good of a job you wanna do, use a dremel, files, or a combination of the two.