Probably pretty clean already, how was the oil that came out of it?, check the oil screen under the fuel pump for debris, if its clean then I would suspect you have little to worry about. I used a pint of Marvel Mystery oil the rest a heavy duty oil, use heavy duty oil(diesel rated) any others may contain additives and you don't want to contaminate the clutch plates, not sure what auto trans fluid has in it, probably OK since trans has clutches.
Think the first run in mine was 500 miles then a drain but I have a diesel car so I just saved it and used it to top off my car with.