Oil climbs all the way to crankshaft. There is a seal between crankshaft gear and front main bearing if I remember correctly, so no oil should get on the gears from the pony crankcase.
I would fill with oil and crank it over with no gas.
Yes, pony crankcase and pinion lube is separate (although if the crank seal gives out, then all the crank lube ends up in the pinion chamber). Level for pinion is on the front cover of the assembly.
The gear and shaft is kind of high. The shaft has a hole to get drip oil from the gear turning. Fill it with auto transmission fluid. (flows easier). spin it over to get oil up on the gear. Stop and let it soak in between the bushing and shaft. Don't start it. Do this several times over a few days and then start it. This is what I would do. Everything may work out. Good luck.