Lyme's vaccine is not usually recommended. It may be necessary in a couple of areas of the country but very few. There are posts on YT about it and one by "Kris Christine' quoting Dr. Ron Schultz (an immunologist) about this. That would be worth reading. Here is a site with side effects:
Lyme Disease - VeterinaryPartner.com - a VIN company!
While some vets do push the vaccine, it it non-core and there needs to be a GOOD reason to give it, especially since people are trying to link the vaccine to possible kidney problems and sometimes even symptoms that make it look like they have Lyme's Disease.
As for extreme itching, sometimes a skin scraping doesn't show anything and the dog is treated anyway. Is Maggie still itchy? Did she have a second dose two weeks later? What are you feeding?