remove the bottom plate from the gear box. this has five screws, on the underside of the loco.
it has been years, so my memory may be off, but
as I recall,
you will find ONLY the forward axle is driven by a single worm, and the motor points downward, ie from roof of loco to track.
This axel should be fine. the rear axle however, should be moved (rotated) so as to have no tension in the drive rods on both sides of the loco, ie a touch of play. as noted, check to see that the screws in the rods are not too tight.
there should be a mirror symmetry in where each wheel , and each motor counter weight drive wheel (the ones above the wheels) sit, on each side.
I know this is vague, as is my memory, but this seems to be what I did to eliminate the jerkiness. This TOO, assumes, there is NO excessive wear to the front axle drive teeth, OR, the areas in which the axles sit in the gear box. This should not be a concern at all, UNLESS your rack loco has had a good deal of wear and use, ie heavy loads, steep grades.
be mindful of the plunger contacts against the inside of the wheels when you take a peek. they need to be pushed into the housing (thin flat screwdriver) before resetting the axle into the gear box, should you pull it out.
work over a towel to avoid bits bouncing into unknown places.
pay attention to everything in its place at the time you open it. make a mental note of where contacts are, etc. so you may confidently reassemble.
as with many quartering issues, you may need to try a few times before its perfectly aligned.