My thought was that there may be a condition of fits where the axle bearings are too far together or apart and are stuck there, with a centre to centre distance bigger or smaller than a coupling rod.
If you have all the valvegear off then that system isn't the issue. Are the rods well clear of the crosshead guidebars and motion bracket at all points of rotation/axle travel?
If all is clear then I would take one rod at a time off the engine and see if it is one or both binding.
It is possible for a wheel to slip on an axle and lose quartering, unless you pinned or keyed them in place.
Also check the rod retaining washers and bolt head undersides for galling or burrs, and that there is side clearance for the rods. In theory the crankpins could slip in or out of the wheel too, depending on how they are held in place or if they have a shoulder.
Just some thoughts, hope they help. I can only encourage you to be patient and remove a piece at a time to find the binding by process of elimination. JD