i have never been to SW in the rain but from what i remember, the stadiums for the outdoor shows are partially covered b/c i know that i chose to sit in the shade instead of in the direct sun. the upper parts of the bleachers are covered - at shamu & the otter & sea lion show. not sure about the dolphin show, but i would think that it is partially covered. i'm not sure if the animals perform in the pouring rain???? i would doubt it.
in addition to the outdoor shows, there are a few indoor walk-through attractions like the sharks & penguins.
you can feed sting rays (covered), sea lions & dolphins (both not covered).
there are 2 indoor shows - Pets Ahoy! & a circus-type act (forget the name).
you mentioned the 3 rides, 1 is an outdoor coaster, Journey to Atlantis is mostly indoors w/ outdoor water flume drops & i believe that the other one (forget the name) is entirely indoors.
i doubt it'll even rain for a full day....it usually comes & goes...wear plastic ponchos for the walks in between the attractions b/c SW is spread out.
have fun....i wouldn't hesitate to go to any park in the rain unless it said on a local forecast the night before that it was going to pour all day.