I had to scroll back to be sure, but you said this bike starts and runs?! Amazing. What is your involvement with this bike? If it were mine, I'd remove the entire intake all the way up to the cylinder, then clean and inspect everything thoroughly. I would probably take the clutch side cover off and remove the clutch plates. My guess is the steel plates are corroded and need to be cleaned up or replaced.
I'd also remove the header and muffler to see what water damage happened inside those. Same with the stator cover. You have serious water contamination that sat for years. It's not like you drowned the bike and a week went by before you started drying it out.
All pivot points need to be inspected, cleaned and lubed too; swingarm, shock, steering, both axles. Basically go through the whole bike in order to put it back into service and know it will not get further damaged by such neglect.