1. When you say join them together, do you mean implement them into the game, or connect them together. To insert them, go to Insert Map, and put in the bank and map of where you want it to be. To connect them together, go to the connections of both maps, pick the direction they connect each other in, and put in the bank and map of the other map.
2. You create warp points by going to the Events menu, and change the number of warps to the number you want.
5. (WTF shouldn't this be 3?)Put legendary pokemon on your map by copying the offset of a legendary pokemon in the game, pasting it to a new event (Or already existing event) in place of the offset, and change the sprite number to make it the legendary pokemon you want it to look like.
4. Same as 5 (Or 3), only copy the tree's script offset and change the sprite into a tree.