Shouldn't boost much in the lower gears, so low boost numbers in 2nd is normal. This woosh sound? Was it like escaping air kind of sound? What was you boost doing when it happened?
I agree with you putting miles on it. The more the better. Using it will bring issue to the surface that won't be obvious with it sitting parked. Intermittent miss/knock makes me think injector. I've had two die on my F250 this past year (Lord knows how many miles where on them) and rig ran rough, smoked more, and had a knock.
Broken valve train parts won't be intermittent.
Heath