Donalds, I'd pull the trans pan, and hammer that dent out ASAP. I'd also replace the trans filter in case it got whacked.
Don, I think you a bit light on your trans fluid refill quantity. When I changed the filter on my '01 5R55E I checked the fluid level before dropping the pan and found it to be right where it was supposed to be. Then I measured how much drained out and found it to be 4.5 Qts. After replacing the filter (and adding a drain plug to the pan) I refilled it with 4.5 Qts of Mercon V. After driving around a bit I rechecked the fluid level and if was right where it was when I started (don't see how it could not have been). I don't think the refill quantity would be different on a '99.