Thank you so much to everyone who replied to this one, and tried to help. The problem was as I originally suspected - an "algae" issue in the tank from letting the bus sit too much. I swapped out the fuel water separator filter and put some biocide in, and the bus has been running great since. Took it for a nice long drive.
Also special thanks to the guys who volunteered info on how to diagnose in the future with a laptop. That sticks out in my head and sounds like great info to know. If I ever end up going that route I'm gonna try and come back / find you and leave a special thanks.