On a vanagon, oddly enough a good pedal comes from the rear brakes being properly adjusted. What you are feeling on the first pedal stroke is the shoes moving out to make contact with the drum. The next stroke seats them and the pedal feels "up".
My suggestion would be to crawl under the van and back off the handbrake adjustment rod so both cables are relaxed. Hard to see, but there is a small hole top center of the backing plate where you can get in with a flatblade screwdriver or brake spoon and adjust the rear shoes up some. Once you get them close, if assembled properly should be self adjusting from that point on. Unfortunately, the replacement shoes don't often match the radius of the drum which also contributes to a vague pedal.
With a proper sealed engine compartment, correct timing and fuel, I'd run it flat out all day long. No reason not to. The load and drag will keep you from over reving it.
Clutch pedal not so easy to diagnose. Short of bleeding the clutch hydraulics, it is self adjusting and depends on the clutch to determine how it engages and disengages. If it is grabbing at the top, you might try seeing how much pedal is required so that you can shift it into gear without it grinding at a stop. You might find, it does not need to be on the floor to disengage the engine.
edit: I forgot, once you have the rear brakes properly adjusted, you can tighten up the parking brake adjuster. I like 3 clicks for the brake to secure the van.