I would say reinstall GWX but don't install JSGME, make sure the game runs fine that way first. That way you can be sure there isn't a stray leftover file from the update left on the computer. If it works try loading the older version of JSGME and see what happens. Then do the mods one at a time.
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"Helm, bridge...what are you doing 60 degrees off course?"
"Bridge, helm...coming back from 90 degrees, sir."
  
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