With the bike pretty well disassembled, I decided to clean things up as I put her back together. Dropped by Home Depot and bought a dremmel and some Simple Green. Everything was scrubbed prior to reassembly. Everything looks much better but she's still an old bike and there's only so much shine I could get back (not that I'm looking for a shiny bike). You can see the difference from these pics compared to the disassembly pics. Especially inside of the front cover where all the oxidation was. Once I get everything back together, I'll probably give the engine case another once over.
Everything back on except for the exhaust. Spent Labor day with some 100 grit sandpaper and some elbow grease. Got the pipes all shined up and then hit them with some heat paint. Have some black header wrap on order. I have a triathlon this weekend so I'm not sure how much time I'll have this week. I'd love to get the exhaust completed but we'll see. Here's how they turned out.