I am slow, but the tortoise won the race, right?
I deleted all my links between table occurrences. In the index options of the key fields, I checked the box about building or creating indexes as needed and that worked for the indexing problem. I had been trying to select 'All' for indexing; apparently FMP wants to decide how much indexing to create. I re-established some of the relationships and now the information is looking better- Things line up & no <unrelated tables>.