I don't have any insight into the ANA results other than a positive result is suggestive of autoimmune disorders in general. However, a postiive ANA result isn't diagnostic of any particular autoimmune disorder. Apparently, people can have a positive ANA and have no autoimmune disorder.
https://rheumatology.org/patients/antinuclear-antibodies-ana
Rheumatoid factor (RF) was the first autoantibody to be discovered in people with RA. Despite the name, however, RF is not specific to RA, and there are many factors that can impact RF lab results.

People with a positive anti-CCP antibody will not have RA, but this test is somewhat more specific for RA than the rheumatoid factor (RF). A positive anti-CCP is much more specific for RA if it is present and it is as conclusive as it gets.

All these tests don't result in a diagnosis with absolute 100% certainty. They are more like pieces of evidence that in conjunction with a physical exam and symptoms which leads to a medical diagnoses until additional evidence later on suggests a different diagnosis.

You were lucky that your rheumatologist took you off methotrexate when you had high liver enzymes. My rheumatologist insisted methotrexate was working for me even when my liver enyzmes where increasing. She said my liver enzymes weren't high enough to cause her any concern.

My concern was the retching every morning which I described as "morning sickness." I blamed it on methotrexate but my rheumtologist said it was unlikely to be methotrexate. I might be nauseated on the day I took my weekly dose of methotrexate but not every morning. When I stopped taking methotrexate the retching stopped so that was enough proof for me.

It was so bad, one morning I asked my wife to call into work for me to tell them I was sick. It was past the time I was supposed to notify work about being sick so I figured they would be angry with me. When I asked my wife if they were mad about the short notice, she said they understood because they could hear me retching in the background over the phone. I felt better after retching and was dressed and ready for work so I probably wasn't as sick as I thought.

A year or so later, I was describing morning sickness while being on methotrexate to another doctor. She said it was understandable because my liver enzymes were elevated. I said she needed to tell that to my rheumatologist.