My thoughts thus far:
-though i still dislike the jimmy/hayes story, there is a little more closure to it now thanks to some deleted scenes. I may incorporate some of them. Though I don't want to focus on it too much, that storyline is unavoidable.
-I may try to get the crew onto the ship even faster. Though I like the New York stuff, the real meat of the film begins with the Venture.
-Englehorn, Hayes, Choy, and Jimmy all have some really great deleted scenes i'd like to incorporate. It adds to their characters and makes you care for them more.
-The stampede might go. Or at least be shortened. This would be to incorporate the swamp sequence and the triceratops scene.
-I'd like to replace Ann's awkward meeting with Jack with the deleted scenes, where she overhears him talking down on Vaudeville actors. This also tells you she did Vaudeville, making the New York scenes unimportant.
I have some other ideas too that i need to play with a bit more. I'll gladly take suggestions, too. If you haven't picked up the Kong Extended Edition you should. It's a big improvement over the theatrical cut, though it's still not perfect.