We had a Ports topic, but old school rs gold then people were not posting anymore and it became buried in other topics. There's a place for it in the RuneScape General Section, it might provide answers to some of your questions from members who know more than me when it comes to PoP.
First off, the ships in question: What should I consider improving? The interior of the hull such as the rudder, the Ram (the slot located in the front of the ship, not sure what it's called)
Personally, I prefer to get the deck items first since there are two. When you're planning to undertake a Seafaring cruise, for instance it's more efficient to have two Seafaring improving deck accessories instead of the added benefit that the hull can provide. There are those who argue that the rudder has more advantages because it'll save you time allowing you to go on more trips per day It's not hard to believe it , but I've always conducted ports in a more comfortable and efficient way which is why I always put the an rudder at the end of every port.
Then, the ports themselves: Which ports are worth upgrading? I've noticed that most upgrades are expensive. I've tried to upgrade my office to unlock a third ship, but it's so dreadfully slow to accumulate bamboo.
In the ideal scenario, you'll want to focus on the upgrades that unlock new ships for obvious reasons, which means you're taking the right steps. I'm of the belief that all upgrades are worth it (except in cases where you have more than one upgrade, you can unlock them all , but fire cape osrs you only have one in use at a time therefore, you must choose wisely).