Trek97 - I will definitely look into evaporust. I want to try and salvage as much as I can.
teazer - Thanks for the response and wealth of information. I'll try to address your information by paragraph.
My uncle may have a hone that I can use to clean up the liners. They don't seem to be scored or anything, just pretty dirty and a little corroded.
I've included a picture of the clutch basket, and the sides of the clutch plates, I'm not sure if you can tell what they are from the picture? The pistons per the markings are .75 over and are for a CB77, so to my knowledge the engine has been bored a bit, what is the next step up? I assume the CB77 pistons are interchangeable with the CL77? I have some pistons in my spare parts box, but I'm betting that they are the stock pistons.
The cam chain was replaced 10 years ago, it still is greasy to the touch and seems to be in great condition. The bike was never ridden after the engine was rebuilt. I have included a picture of the cam shafts with the chain.
From talking to my uncle, his father in law had received a CB77 and a CL77 in a deal, both as parts. He may have been blending the two together by the time he gave the bike to my uncle. So that may explain the hubs and brakes.
The motor will be sitting in my room, until the beginning of the new year when I can afford some of the rebuild kits. I've put a little bit of oil on the moving parts to lubricate and protect them, is there anything else I should do? I've referenced the Honda305 forum quite a bit, I'll be sure to create a profile soon.
Here are some more pictures I took of the engine, including markings on the pistons.