Misfires can definitely damage the TC and input shaft splines, depending on how long it was driven with the misfire condition, severity of the condition, etc.
Trans will need to be completely torn down as if it was a new job, everything inspected, tested and, where applicable, reconditioned or replaced. TC failures like that are generally catastrophic insofar as LOE to restore the trans to new build condition again as the pump's working surfaces often sustain damage and need re-machining or replacement.
Let us know what happens once the builder has it and gets back to you...