Lupus and scleroderma ( I have both) are not always easy to diagnose but eventually antibodies show up and there are general inflammation makers like sed rate that show up, often first. There is a specific lupus panel that is run and doctors also will look for the antibodies associated with scleroderma.
Northwestern, Rush, and U of Chicago all have strong departments of rheumatology if you decide to pursue your idea. But if you are not having some of the clinical symptoms of those diseases you probably don't have them. If you had an AI disease strong enough to destroy your colon I would think you would have a collection of symptoms and various lab results would have had results to investigate further.
MCTD (SLE Lupus, polymyositis, scleroderma). Diagnosed 2005. Kidney, liver, GI tract, dysphagia, raynauds, barretts esophagus, quadriplegic in 2005. Recovered and now active in downhill skiing, golf, hiking. Meds: amlodipine, benezapril, omeprazole, potassium, folic acid, vitamins, maxide.
Remain Optimistic and you can overcome.