That seal is quite easy.
Pry old one out (I use a light hammer and a small common screwdriver to raise the lip, then twist-pry with a bigger screwdriver), clean the bore, put black RTV or gasket sealer on perimeter of new seal (where it touches the trans bore) and tap it in with a large socket. You WANT RTV to splooge out from under the metal lip.
It can be hard to get the new one started straight. I've found that even when cocked at the beginning, as long as you keep the socket driver seated, it'll drive the seal in straight with a couple good whacks. Buy two seals for good measure, they're <$5.
Be VERY glad you caught that. I find it hard to believe that an 04 would still have rubber shift rail plugs....