It has been quite a long time since I have had much time to work on my project, but I wanted to summarize up the past several months efforts. Having a child will definitely put a damper on project time.
During this time I have been working to get the Engine sorted out and ready for installation. This effort includes disassembly of the entire engine, cleaning stripping and repainting the engine cases, and reassembly of the engine. During this effort I would be replacing the bottom case of the engine as the original one had a leak. I would also be replacing the head with one that has all of it's fins as the original one had several broken ones. Here is a photo of the engine before I started:
Notice the broken fins and dirty corroded and scuffed valve and side covers. When I disassembled the engine I planned to also replace the valve cover and side covers, or polish and refinish them. Disassembly went quickly and honestly was done in about 2 hours. I had done an rebuild before and it goes quickly when you have some experience. I bagged up and labeled all the parts and prepared to clean up and refinish the engine cases. The next big step was to get a new head and bottom case. I bought a head off Ebay that had all fins and was from a running bike. I also bought a complete case locally from another enthusiast and was ready for my rebuild. Sometime during the spring I did the massive cleanup of the cases. I took the top and bottom case and used a serious degreaser to remove all of the outside crud. This involved a few hours of scrubbing and elbow grease, but in the end I had parts ready for paint. I then masked them up and painted them over the summer with VHT high-temp satin finish barrel paint. I also purchased an Athena gasket kit that includes all gaskets, seals, and washers you need for a complete rebuild.
The head I purchased was very dirty and would be very difficult to clean, so I found a local shop that was willing to use their sandblaster to clean it up, and they also stripped off much of the outside coating as well. This was a very worthwile step as I don't think I could have possibly cleaned it sufficiently without doing this. The final head before paint can be seen in the picture below as I am reinstalling the valves and installing new valve seals. I polished up the valves and removed all carbon deposits, and also refaced the valve faces with laping compound. I then masked the head and painted it.
Once repainted I began reassembly. There are a few photos below that show some of the stages, but mostly this was a fairly simple process if you follow the manual. Notice the nice new finish on the outer cases and cylinder. Also notice the new copper gaskets on the bolts that hold together the top and bottom cases. 
Next I will install the engine into the frame and rebuild the clutch.
