Connecting the symptoms

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I'm a 36 yr old female with two small children aged 2yrs and 4 months. Eight years ago, I was diagnosed with Hashimoto's Thyroiditis and have been increasing my synthroid regularly.  Two years ago, I donated blood to find out I have elevated ALT.  I went to a specialist (gastro) which did further blood tests.  They found speckled autoantibodies and decided to do a biopsy.  The biopsy at the time said it was fatty liver.  I don't smoke, drink, do drugs and never been overweight (except when pregnant).  I'm pretty active with two kids and otherwise I'm in good health.  Since that time, my ALT keeps rising and is 129, my AST is 59.  I went to the doctor again because the fatigue was getting worse and I started to experince joint pain in my hands and arms.  No swelling, just pain that would come and go on certain days.  He did some bloodwork and my ANA came back positive 1:160.  This time they sent me to a rheumatologist, my x-rays were normal with some minor issues with my knees, but didn't show any joint damage.  He said I could be one of the few that has a positive ANA with no known disease.  The pain in my hands is mild now but does flare up a few days a month.  Of course, I try to keep in mind that I have two small kids and being tired all the time and joint pain comes with part of the job.  I have noticed that I have to get up several times at night to urinate like I'm pregnant, but I'm not and I sweat at night too.  I wasn't sure if this was just post pregnancy issues or not or if this is somehow related.  I've been through all the blood tests and don't show any viruses that would be causing this.  Could it be that I'm just one of those people that just have a positive ANA and higer ALT than most?  Can it be related to being pregnant?  I had my gallbladder removed 18 years ago so it wouldn't be that.  I just think it's odd that I have a autoimmune disorder with my thyroid and now my ALT has been elevated for the past couple of years and a positive ANA.  .