Had lower back pain since 2018, i have done mri's, physical therapy, emg, etc. all normal. ana was tested to rule out lupus, the ratio came back borderline, ~6 months later with the worse pain, my test is negative. why? could it still be autoimmune?

ANA is a sensitive test but not specific at all. If you are concerned about you current condition, please request a rheumatology referral. Good luck.

Suggest a visit with a physiatrist and find underlying answers to explain your chronicity. It is not feasible to provide clear-cut answers here, but more likely a rheumatological or structural issue. You might consider genetic disorders. Based on the data provided, an autoimmune condition does not appear likely.