MAER,
Welcome to the Stovebolt. I would guess you have air trapped in the system, but replacing the thermostat would be a wise move too. Exactly why your top hose collapses, I am not sure...maybe the pump is high output, and because the stat isn't open, the pump is creating a vacuum on that side of the system.
Drilling a hole in the flange of the new thermostat might alleviate any future 'burping' problems.
The air cleaner can collect oil from a crankcase venting system that might be plumbed into it. Check your PCV valve and any related hoses.
Stuart
