The genius behind this model is that you did not have to remove the siderods for replacing the traction tire. The #4 driver (the rear one) has no crankpin, so you can slip the tire between the wheel and the siderod. Yeah, this info comes a bit late.
I don't have the loco in front of me but I believe you are describing the main crankpin which which retains the main rod and has the eccentric crank. That crankpin is likely keyed so it only fits one way.
As for quartering unless you took the drivers out of the mechanism, there should be no problem. The only geared drivers are #2 #3 and #4 and #1 is free spinning. There are only 2 crankpins. Small one on driver #1 and the one you having problem with on #3.
If you have another Mikado, use it as a reference. If not, here is a photo to use as reference:
