Good suggestions, thanks. I think the easiest thing for me to do would be just to make my own theme at this point. I've never web optimized for iPad before and I had no idea that mobile safari wasn't capable of proper div positioning/overflow. To make up for that, I ended up doing the two-finger scroll method.
I found a script here as a solution for that but I have no idea how to implement it:
http://cubiq.org/iscroll-4
Edit: sorry to everyone else about the nerd speak. There's no other thread for iPad web dev so hopefully I'm not derailing too much