Could high calcium in the blood and intake of levothyroxine for hypothyroid be cause of strong foul odor in urine? i drink ~3 6oz cups of water a day

Unlikely: Neither high calcium nor levo. Will cause foul odor. Most common cause of dark, strong urine is dehydration. You should be drinking minimum of 100 ounces of fluids/day or enough to keep urine color fairly clear, not only to help lower calcium but to prevent kidney stones . Other causes of foul urine are UTI and certain foods and meds. A urinalysis and culture can determine if UTI present.

Malodorous pee: First of all, you need to triple you water intake. I think the smell may be as much from its high concentration then from T3 or hypercalcuria.