That's why I don't like using the bypass valve, it's hard to know how much oil is bypassing your 'fuge. Anyway, for peace of mind, is it possible for you to direct the centrifuged oil into a bucket or something similar? That way, you can guarantee that all the oil going into your truck has been 'fuged and even if it only has one pass on it, that's better than no passes at all.
As for the filter, clogging up two isn't uncommon so you'll want to get a couple more filters just in case.
To your initial question of the thin layer of contaminates, my fuge will continue to pull stuff out no matter how long I run it. By the nature of the design, there's always going to be some buildup on the walls of the rotors because there'll always be something in the oil (not necesssarily a contaminant) that's heavier than the surrouding oil, make sense?