If you need to persevere with the harness, I would go right back to basics.... so get the harness out, if she doesn't react - click-treat. Gradually get it closer to her, and again click-treat any lack of reaction. Once she will sit calmly with her focus on you with the harness on the floor beside her, begin to work towards getting her to wear it... again take very very tiny baby steps... (Obviously, if this conflicts totally with the advice of your behaviourist, then ignore me... I'm not an expert and I haven't seen Lily!)
It could be that her tooth was knocked at some point putting the harness on, so she may associate the harness with an increase in the pain in her mouth and while the pain may be gone, the association will still be there...
As others have said, finding a different way to transport her may be the better option (at least in the short term!).
Glad to hear things are going so well generally!!