This would also be a good time to upgrade to the 96+ pan for the deep sump, and if you want a drain plug then get a pan from a truck as they had built-in drain plugs. If you go this route be sure to get the correct filter, as a stock 95 filter will not work w/ the deep pan. Maybe also add a tranny cooler to help keep that thing cool.
And of course, when you re-fill it, use Mercon V in it, not Mercon III.
Did you empty the torque converter of fluid as well?
Post up a request in the Ford Parts Counter forum for that shaft seal you need.
These are highly engineered precision vehicles, the first step in diagnosing the problem is to strike the suspected offending part sharply and repeatedly with a blunt object, then re-test.