I have painted the inside of my CB350 and Sanglas pipes. It is quite simple, or so it seems. Just use masking tape and kitchen wrap. First, cover drain holes or any hole with masking tape. Then, wrap the pipe with kitchen wrap. Open both ends and protect with masking tape.
Now get alu-zinc or any of those spray can galvanizer, and paint away. You will probably be unable to paint the whole pipe, because the baffle inside doesn't allow the paint to cross it, and also because the space is so confined that the spray doesn't have space to "open" and cover a bigger surface. Anyway, paint away and when you are done, leave the pipes resting in the same position as installed. I did that because I thought that, if there would be paint runs, it would be better that the excess paint rests where it is needed the most, that is, where the condensated water will be: in the "bottom".
I have painted those pipes when used, that is, over the carbon and rust. Zinc galvanizer is suppoused to neutralize rust, and if it falls upon carbon, then there is nothing to worry. Apart from that, I pour in my tank a good dose of motor oil every now and then. I tried two-stroke oil but it is so clean now that it doesn't smoke at all. I pour regular, mineral oil. It burns with more smoke and it is cheaper.
Those two things are buying me some peace of mind. Time will tell whether they work or not.