This is a brief list of things I got stuck on, and how to get around them.
Rope
Rope can be crafted with two leaves.
Nails
Nails can be crafted from two scrap (which is found in barrels or on the sea floor)
Sand, Clay, and Giant Clams
Sand and clay can be found on the sea floor, and are mineable by using the hook on them (Hold it own, it will begin swinging, like a pickaxe). Giant clams are collectable by interacting with them.
The Islands and other Rafts
On your journey you will sail past islands and other rafts. You can use a paddle, or a sail, to head to them. For other rafts, try ramming into them and wedging your raft onto them as well as you can, as it will drift away. Collect the crate and then get back onto your raft.