I guess first thing I would try is to pop off the lead going to the blower motor, then hook it to a multi meter and run the switch through its range of travel several times to see if you have any dropping out.
There are only so many things to go wrong in this system, so if the blower is known good, and all the associated components check out good then look for things like a fan impellor hitting on the inside of the housing, also check for any loose or damaged connections and any wires that may have been damaged or possibly broken inside the insulation. (that one will drive you nuts)
So if the fan switch checks out good and after several times of turning it on/ off and up/ down then start wiggling wires and connectors. If the switch checks out good then test the blower motor again.
An intermittent problem like this will about drive you nuts. Basically you need it to be in FAIL mode and then you can find the problem.
Good luck with it.