Hi Paul, it's quite difficult to envisage your setup, do you have a picture?
2" does sound like it's a bit close to the floor. I drove Sherpa Vans across Europe in the 80's and don't remember there being any particular issue with the throttle pedal.
The only picture of a pedal box in-situ that I could find was in this Sherpa V8 conversion thread, and it doesn't look like there's such a big difference in pedal heights -
I'm a big fan of floor pivoted throttle pedals like you find in the Triumph Vitesse and Herald. The pendulum throttle pedal in my MG sits too high for my liking - when my right foot is in a comfortable position for cruising, if I then floor the accelerator without lifting my foot first, the end of my foot drops off the bottom of the pedal so it pops back out and I lose all the go. That just can't happen with the Triumph floor pivoted type.
Anyway, good luck sorting out your pedal box.