Loin pain hematuria syndrome (LPHS), possibly autoimmune

This is going to be a long-winded discussion, but please bear with me, as I really need some help. So this all started when I first had an episode of hematuria around the beginning of August after presenting with right flank pain. I went to the GYN and there, she ruled out cysts and found hydronephrosis on an ultrasound. Kidney infection was ruled out, and a CT scan with contrast was preformed where no abnormalities except for free fluid on the left from a ruptured ovarian follicle- 2x2cm. Underwent a cystoscopy and stereoscopy with my urologist where they found a mild UPJ obstruction and they placed a stent which caused too much pain itself to tell any improvements. I then had a renal scan with Lasix where there was no evidence of obstruction other than mild dilation. I then was sent to the Nephrologist where bloodwork was preformed that showed positive antinuclear antibodies and positive rap antibodies, and I can also see that Urine WBC was high and there was trace bacteria in the urine as well as proteins and ketones with 2+ blood. My serum myoglobin was also low. A biopsy was ordered to test for possible lupus, but findings came back completely normal; no abnormalities in glomeruli or anything.

As of right now my diagnosis is Loin Pain Hematuria syndrome, which is pretty rare and a depressing diagnosis with the only thing to help is pain management or an autotransplant. As for my symptoms, I have reoccurring hematuria, as well as chronic right flank pain that gets worse with physical exertion. The pain has been increasing and is impeding on my daily life. I have decreased energy levels, high thirst, more frequency and urgency with urination, occasional low appetite, slower healing wounds, brain fog, swollen lymph nodes in neck, and I have always had trouble swallowing which I know is related to some autoimmune disorders. I have a history of asthma, anemia, and possible Raynaud's syndrome, and a family history of kidney stones, lupus, PCOS, Addisons, and Graves. I could really use some help on this, I am going to Mayo to get a third opinion. I am not sure if finding the antibodies was just a chance finding and I could show signs for an autoimmune disease in the future and it is unrelated to my renal issues, or if there is something we are missing.