I’m used to 7mm, and pre-quartered wheels, but I’ll offer a few suggestions.
for a 4-coupled chassis to run sweetly, you need
Axles to be parallel in plan view (they occasionally may not be in front view if one is equalised)
Coupling rod centres to be same length as wheelbase, both rods identical, of course.
Quartering to be identical on both axles.
Crank throws to be identical on all four wheels (ok, they could be different on each side, but…)
Sufficient running clearance in axleboxes and crankpin journals.
Clearance between wheel face (and any protruding bits & pieces) and back of rods
The running clearances will need to be more generous if your loco has suspension a/o equalisation.
so, an approach; there may be others, whatever, try to work through it methodically.
Remove gearbox, remove pickups, remove rods, does the loco run sweetly, and straight, down a gently inclined smooth-ish piece of wood?
If it doesn’t run smoothly, check bearing clearances, if it doesn’t run straight, check the axles are parallel.
Put rods on, chassis on track, get a very weak elastic band and a bit of wire, pull it along gently, locate the binding. Is there more than one point in each revolution?
is something catching? Axle, balance weight or hub on back of rod?
referring to one side, if it’s binding at 12 & 6 o’clock, I’d guess there’s a mismatch of wheelbase and rod centres on the other side. If it’s binding at 3 & 9 o’clock, it’s the side you’re looking at.
If the binding is at 45 degrees…. Mmmm, must be a combination of things. Swap the rods, just to check it’s the same.
I’m not conversant with how crank pin bushes are arranged in 4mm, but I only clean the holes in the rods to ensure they’re smooth, if I need more clearance, I would turn down the bush to get it, because if I make a bollox of it / overdo it, a bush is pennies, the rods are not so easy to replace.
hope this helps
Simon