I have learned to drop the valve body (even with trans in car) to facilitate seal replacement.
Make sure the top of the seal area on the trans is clean and your shifter shaft is clean without damage. I also use a bolt, washer and socket to pull the new seal in. This is such an inexpensive seal, but it can cause so much anguist if it leaks again. I would also replace the front and rear seal (with boot for slipjoint).