If you are having soil issues, I would repot. There are mixed opinions on doing that this time of here - some of us do and some don't. I think if all the lemons are off and the tree is healthy, it should be fine - especially if you are moving it to a better mix. I would not totally bare-root now, just shake off the dirt you can manage without hurting the roots.

You can also spray the top of your new mix with a neem oil solution to keep the pests at bay.