A quart of fluid WILL come out of the small pan, AND you must replace a quart of fluid IN that pan before reinstalling it. It can be a bugger....but yes, that little pan can get nasty too.
Your alt should read nothing less then 14V while UNDER a load, i.e. heater/radio and anything else on that you can think of. If it reads anything less it's failing and thus causing the tranny to run ineffectively.