Well, removing the coil is NOT the first thing I would have done and not the first place I would look for trouble... but since you are already there, get yourself a copy of the Lionel service documents (Easily Licensed/legally available in the Greenberg's Repair and Operating Manual for Lionel Trains: 1945-1969 publication or via the LCCA/HSL Digital Archive). From there, you can see the schematic (sampled below) and exploded diagrams to be able to check for unexpected shorts in the 4 secondary winding sets:
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