Giving you my sympathy here, I have the exact same problem. Because of my phobia for falling (not heights, it's totally different) I was terrified of thrill rides all throughout my youth. When I was 16 I finally decided that I couldn't be a wimp anymore and just started riding all the rides with stomach turning drops on purpose. Now I've been on some of the largest drops in the world (living fairly close to Cedar Point helps), but I still hate them. TOT is my nightmare ride becase you can't even tell when you're going to drop, but I ride it every trip (several times

) because it's my DH's favorite.
Anyways, here are my suggestions to make things a little better:
1. Scream. Or, at least, exhale just before the drop. It helps, but I'm not sure why.
2. If you can, sit in the very front. This won't help with TOT, but you could do it with Splash. It helps with your mental preparation to be able to see where you're falling. Plus, at least with roller coasters, the front car actually goes down several feet prior to beginning free fall, so you actually fall slightly less.
3. Go with friends. Make sure they're good friends who will keep you laughing throughout the ride and not thinking about the big finish. Also, make sure they know about your fear and are the type who, if necessary, will get tough on you. There are times when peer pressure can be a good thing.
4. Remember to enjoy the rest of the ride. Look at all the themeing. Have a reason, beyond the drop, to go on the ride again.
Oh, and this is just a note, but I think that the "bouncing" drops of TOT aren't that bad. The first drop, you get the full stomach treatment, but afterwards you go up and down randomly. However, the parabolic up and down motion makes for less of that 'ugh' feeling than a straight drop gives. It's a slow transition from going up at a certain rate of speed to free fall and I actually don't mind it too much.
*Edited because I forgot one thing: The larger a drop is, the easier it is. I know that sounds crazy, but after you reach a certain height (something like 300 feet) your stomach actually has time to catch up with you. Then you're just falling and not feeling anything. Very weird. Unfortunately, there's nothing that big at WDW, but something to keep in mind for the future.