Do you have the actual test results for the various tests that have been done? Was Molly treated for Lyme? If so, when was that and have you had her titers checked after treatment? Is Molly currently on Prascend or Pergolide? If she was on medication when she was tested in February she wouldn't be negative for PPID but her ACTH level might show that her PPPID was being controlled.
As her current soreness started in the same time frame as the fall rise it sounds like her ACTH is not well controlled with Prascend (if she's on it) or she's in need of a dosage adjustment (if she is being medicated). Having the vet pull blood now can be tricky but at least would give you some guidance on where she's at right now.
If you can post current trim pictures and any x-rays you have we'll be able to advise you on her trim. If she's sore, as already mentioned, you should not be making her move. If she's comfortable moving in her area to get hay and water that's fine but no forced exercise at this point.
If she's IR and/or PPID you need to remove the triggers to help her feel better - that could mean changing her diet and/or medication - we'll be able help you sort that out once you have a case history done.