Okay, so I can answer all of these questions, but I also wanna refer you to Nick and LTM's ZC tutorial. It's a bit out of date at this point, but it should help with the basics. Now, to answer your questions...
Warp whistle points: you'll wanna go to Quest->Misc Data->Warp Rings, and edit the first one in the list. The whistle will only warp you to a point if you have the corresponding triforce piece.
Raft: The raft is a passive item, rather than an active, so you can't select. It'll only start moving if you walk onto a dock combo, and if raft flags are placed over the water.
Talking to a zora: This one is by far the most complex. The easiest answer is "Use a script," though if you're using 2.55, a signpost combo may work. Either way, I'd really recommend getting the basics down before jumping on this one.
Push blocks: You simply have to put one of the push flags on top of a solid combo. If the combo type is "Push, wait", it won't move until enemies are dead. The type of push flag determines how it moves (vertically, horizontally, or all directions, and if it can only be pushed once or repeatedly). If the flag says trigger, secrets will trigger when the block is pushed.
Zelda 2: Yes, go into the screen data (Press F9 or Screen->Screen Data), and check "Sideview Gravity" under room type.
Hookshottable block: Make the block's combo type "Hookshot Grab".