I had terrible neck stiffness and back of head pain at the base of my skull. In my case, mostly babesia related, has gotten a lot better with treatment along with most other symptoms.
I think it's fine to do some herbals before your upcoming protocols since they seem to be so helpful. But personally, if it was me, I would initially not take herbs as I start the protocols so I can gauge how Dr J's program is affecting me. If the response is severe and strong, I don't know if having extra herbal antimicrobials is a good idea. Now if you find you are tolerating the abx regimen ok, I think slowly stacking a few herbals on top is probably relatively fine. But read up on the herbs to make sure there aren't any known contraindications.
Do you have any of Buhner's books? I would recommend getting those, both the lyme and coinfections books. You could start researching and reading those, they are a fount of useful information and will help give you a good foundation to work from in regards to herbal treatment strategy.
I've found herbals very useful, not enough on their own, but useful nonetheless. Some of the most effective for me have been Zhang brand allicin, houttuynia, artemisiae. Neem, liposomal artemisinin, oil of oregano capsules, CSA formula from woodlands essence, nauclea latifolia also all good.
The Byron White formulas are also good options. I've found A-bab to be very effective. I didn't respond to the other formulas as much, but as I've mentioned before babesia is very likely my dominant infection. This page has some info on the formulas: https://www.gordonmedical.com/byron-white-formulas-guidebook-table-of-contents/
If you want to order the formulas, I know a site where you can get it directly, feel free to email me if you'd like the link.