Hey guys,
Since I found your thread I figured I'd update you both here. Turns out it was in fact with the pinion gear. Unfortunately in order to remedy the "problem" I had to remove a side to access the pinion. Thinking it was an adjustment with the shims on the main shaft, since the kit gave me two different sizes, I tempted the make the adjustment there, and because the motor shaft relief for the pinion set screw was very small I didn't think that would make up the difference.
To resolve the issue after removing the side, I removed the spacer from the top bearing of the main shaft, then moved the pinion up the motor shaft as far as the relief would allow. I didn't need the shim on the main shaft. After seeing it all in perspective it is very simple, obviously. My only complaint at this point is in the manual. The foot note in the manual should be on a page or two earlier, not after you have the frame assembly completed. Unless you have specialized tools, which really is not necessary, you don't have room to access the pinion to loosen or tighten the set screws once the frame sides are assembled.
For me the easiest way to set the adjustment of the two gears is to install the motor, mount & pinion, and main shaft bearings to one frame side. Position the main shaft and gear in its bearings, then make the height adjustment and shim placement at that time, then attrach the second frame side and confirm their position. Had the foot note about the required position of the gears been on the page with the assembly of the frame you could be prepared to make the gear adjustments.
Fortunately in the end all is good! Thanks to both of you for all your input!