Its best to get another transmission. You can rebuild it but it will cost more than its really worth. Are you sure the whine is coming from your tranny and not the rear end? Second what oil was used when they flushed it. I personally only use RP 75W90 in all our miata's in both the rear end and the tranny. If its still shifting fine you probably don't need a new tranny, the synchros generally die before anything else in the tranny.