Do you think all connective tissue diseases (lupus, sjogrens, scleroderma) are more alike than doctors realize since they tend to overlap so much?

Yes and no: Autoimmune diseases are all as different as the people who get them. These conditions all result from the body's immune system attacking different parts of your cells and tissues. Each person's disease will reflect the tissues that are being damaged. It is likely that everyone who has one of these conditions has a different spectrum of tissue damage which may be similar in some ways..

Related: Autoimmune disease such as lupus and Sjögren's syndrome are indeed related by the fact that it is the immune system that is attacking the body itself. However, different disease have different but overlapping targets of the misguided immune attack. For example, there can be joint pain in lupus, a symptom that overlaps with rheumatoid arthritis. However, the joint involvements are different.