At the end, I found a small can of rust pain in my garage that says flat. I use a small drop to touch up the bare metal area of the ring and it looks great!
For the objective walls, I actually used the permanent marker. My thinking was, the glass walls are matte ground glass so even though, the marker ink looks shinny on flat surface, it should not be reflective on the objective walls, especially when the light is projected from inside the glass.
The lens is back in one piece. A dirty lens with fungus grown inside turned into a shinny, like new looking lens. This is my first 28mm f2.8 AIS (with CRC) and a quick test yields excellent results! I will need to check and possibly adjust the infinity tomorrow as the last step. Luckily, 28mm has very convenient infinity adjustment that does not require too much of disassembly job.
All in all, I am pretty happy with the project. Thanks everyone for your inputs.