so was I right to start the Skull Island portion on the morning of the 5th day?
Yes, that's correct. You spent four days at sea, and then on the start of the fifth day, you reach the island. (This is assuming, of course, that you chose to head for the island and made progress each day. Weather effects or stopping at an island can make a "four-day" trip take longer. For instance, if you roll that it's a four-day journey, but on two days you fail to make progress, then you won't reach the island until the morning of the seventh day because it took you six days instead of four.)
Likewise, when you say that "you may decide not to try to make landfall after rolling", is that after rolling for progress or rolling on the small island table?
That's after rolling on the small island table. For instance, suppose you decide to try to make for a small island and roll that there are rum runners there. Peering through the spyglass, you see them and their ship at the island. You may choose to not make landfall, but that means you also can't stick around after encountering them to repair your hull. Or you can go ahead and risk it if you really need to repair your hull. Then, it's up to your Lookout to determine whether you have to fight them or whether you can evade them.
But perhaps what I should do is just have you roll on the table and not give that option; presumably if you go looking for an island, you'll explore one you find. That would certainly make the "attacked by warriors" encounter more likely.
If you choose to press onward, you roll for an ocean encounter, but if you choose to search for an island and fail the progress roll, do you then roll for an ocean encounter?
As you mentioned, the rule is that if you did not stop at an island, you roll for an ocean encounter, so yes, in that case you would, because you did not stop at an island. (In the above example, too, if you choose not to make landfall to avoid the rum runners, you'd also roll for an ocean encounter.) Basically, if you're not walking around on an island, you're going to be rolling for an ocean encounter. But perhaps that can be made clearer!
I'm having an absolute blast with the game. These are just a couple little issues that haven't hurt my experience whatsoever, but could be good to address in a v1.1 update.
Well, thanks for saying so - and taking the time to say so. Glad you're enjoying the game. I'm taking notes for a future update.