Mike, honestly you won't need to use heater boxes if you install a gas heater. I do like the fact that you'll be using the existing ductwork for heat and defrost. And the combustion intake and exhaust can be neatly routed under the car if you install over the trans. Good on you if you take the plunge. It's a lot of fabrication, but from the work I've seen you do, you're up to it.
I recommend that anyone with a gas heater only start them when the engine is running. The glowplugs draw a lot of current, and the alternator really helps with that by boosting the voltage a bit. Heater startup is a lot faster when the engine is running.