Shawn,
You can swap the connectors at the motors. They are electrically identical, though of course the meters will not read correctly. If the problem follows the connectors, then it is something in the control box, cables, or connectors. If not, the motors.
One thing you can check at the shack end is the 3 wires to the motors. Lines 4, 5, and 6 should all have continuity, with a few ohms showing. "Few" being something like 5 ohms. I can't find my notes with the exact numbers, and they will depend on the length and type of the lines.
If everything checks, then it is _probably_ the 100 uF phase shift capacitor you can see between the windings in the schematic. You can get a replacement from Yaesu for $10-15 including shipping. Replacing it is not hard, but it is very tedious and messy. Unlike other versions, the G-5500 has the capacitor in the motor housing rather than the control box.
I had exactly the same symptoms you describe, and it was the capacitor in my case.
Good luck,
Alan WA4SCA