It's possible there is dirt from the water left over in the trans screen.

Many a Aisin transmission has been flooded and brought back. Take it to a shop for a flush and fill make sure to have the Trans filter/screen cleaned each time. After the flush and fill drive it around to help burn off the excess water, should take maybe 3 times to get it all. Expect boil overs and possibly fires from the oil and water coming out the dipstick and onto the hot exhaust. You'll get it back in order.

1999 Montero SAS'd on Kings and stuff

1998 Montero trying to get a V8 Swapped