Well you can solve that problem - take photos of your gears as you assemble it, and post them here

I wasn't able to find a good photo of the three hubs, only the 1-2 hub

The main drive gear is involved in "4th", but is not 4th gear, rather the main drive gear drives the cluster shaft gear. 4th "gear" is actually the input shaft locked to the main shaft, so the input to output ratio is 1:1. The two key parts are the 3-4 Synchro Hub which is splined to the Main shaft (output shaft) and the Main drive gear which is locked to the input shaft. When the box is in 4th, torque is not transmitted via gears