Have low back more of cramp nagging pain like the ones when starting labor + headache, on and off for a week. Urinalysis normal. Is it pyelonephritis?

No. Pyelonephritis (kidney infection) would be associated with an abnormal urinalysis (many wbcs) and symptoms of fever, chills, flank pain, and feeling quite sick. Your symptoms and normal urinalysis are not consistent with this.