some of the automatic trannys don't circulate fluid in neutral. Whenever I replace one, as stated, put fluid in till it shows the proper level on dipstick, fire it up, shift into reverse, then drive a couple times, back into neutral, and check fluid. Repeat till it shows on the dipstick but is STILL LOW. You want to do your final level check after it is up to operating temp. You should also be watching coolant at the same time.
One more thing to add, I am assuming since you said it was a stock engine, it does not have roller lifters. You should run oil with zinc additives in it for proper cam/lifter lubrication. They have taken a lot of those additives out od the oil in the last 10 years and it is real hard on flat tappet cams.
