1. It's kind of more the storys of those games that I'm combining, not so much the gameplay. It's still going to be cave story physics, but many zelda themes will appear.
How much do you have already planned? The engines/gameplay for Cave Story and various Zelda games you've listed are drastically different in style (MM and OoT are 3D, for one), what elements from these Zelda games do you plan to implement and integrate? If dungeons will have a lot of puzzle elements like Zelda, keep in mind that you'll need some decent coding skills. Are you recreating dungeons from Zelda into, or designing them from scratch? How will the storylines be merged together?
I could be completely wrong, but it doesn't sound like you've really developed how you're going to go about this project, and this sounds like a big project. I'm not trying to dissuade you from continuing, just make sure you know what you're doing before you do it, or you're in for a lot of unnecessary frustration.
2. I haven't really worked on the dungeons to much, but I am going to try to recreate them. But I will edit things so it will work with a side scroller perspective.
Also I love Zelda 2.