Locked in refi rate, payed appraisal, delayed closing 75 days re-ran credit, and DONT qualify?

Credit reports do have to be rerun if they get old enough, and lenders must use the most recent scores for underwriting and pricing purposes. It is never good when the loan process stretches out as long as yours did, but (particularly with big servicing banks) it often does so. If your loan officer did not tell you what caused your score to drop, please ask him. It may be something as simple as you maxing out a credit card or something else you can fix and salvage your loan.