Katrina, I wish I could suggest otherwise, but any pitting at all is going to require a bore job, and unless you want the motor to shake your teeth loose, that means boring both cylinders and replacing both pistons to keep pistons and bores uniform. 5twins has given you sound advice: a machine shop can assess the cylinder damage and tell you what needs to be done. Make sure that the bronze colored coating is intact in the connecting rod small ends.
Before you spend a dime on the top end, you might want to find out how far the water penetrated. If it was my motor I'd split the cases and take a close look at the main, big end, and transmission bearings. There's a fine thread (search and you will find) on locating the case fasteners. Loosen a little at a time in book sequence, highest numbers first, turn the motor upside down on the bench with the cylinder studs hanging off the edge and supported from the floor, and remove the lower case. You may need to apply some encouragement with a few taps on a wooden drift, but the lower case half usually comes off without a struggle. You'll need to break the cam chain to remove the crank assembly. The tranny shafts lift right out.
A lot of folks wouldn't go this far with inspection, but it's better to know if you have low end and/or transmission issues going in than to find out the hard way after you've spent a lot of time and money.
Good luck, and welcome to the asylum!
