Cindy,
I had iontophereisis after wrist surgery and it helped, but that is dealing with much smaller muscles and tendons. I had it at PT after knee surgery (ACL/MCL not replacement) and it did nothing - doc said there is too much tissue/scar tissue for it to penetrate when done at safe levels.
Have you tried Voltaren/Naproxen gel or cream instead of BenGay on the knee? It is an actual NSAID, but most of it stays right in the tissue, so no stomach issues and limited affect on kidneys and/or liver.
One thing I learned using anti-inflammatories - even topical ones - is to do it consistently - they are more effective if used a few times a day instead of waiting until I ache.

You have had a long haul, but you'll get there! Kudos to you for not giving up.
Sue