Yes porting can be done free hand, but try to make it look nice. Any bit for grinding metal, probably a rough sandpaper bit to start with, down to finer ones to finish it off nice and smooth.
Also, carbs can be ported. So a 12mm Gurtner can be ported up to 13 or 14mm.
Really, the first thing anyone should do to their bikes is called blue printing, which means making everything as it was designed to be, as the manufacturing process has a lot of errors. It includes cleaning up rough edges etc. So you will probably find some of those in your engine, clean them up a little, and you will have a feel for how the metal grinds away.