Pearl Harbor can have busy days and sometimes all the boat rides for the day can be issued and gone by the morning. So keep that in mind. If you plan to do both the same day, they are about 10 minutes apart, I've never done this so you need to research if it is an option to get boat tickets for a set time later in the day. If so, go to Pearl Harbor and pick up tickets, then go to the Swap meet, have lunch and then go to Pearl Harbor.
I see you took out the zoo, probably good. If you have been to other major zoo's, this one will be disappointing to you. It is doable in maybe 1.5-2 hours though. The Aquarium, it is almost right across the street as has some beautiful fish, as well as Hawaiian Monk Seals. You can visit the Aquarium in about an hour.
I suggest you look into driving out along the route towards Hanauma Bay, Sandy's Beach and Makapu'u Lighthouse. That in my opinion, is one the most beautiful drives on the island.
In planning your driving, keep in mind although the miles traveled may not be far, it takes longer to get around. You will not really be wanting to be heading back to your hotel during rush hour traffic during the week from Waikiki. It will be bad. The same goes for leaving Aulani early in the mornings to head to Waikiki/Pearl Harbor. There is basically only one way in and out of the area. Weekends this really isn't an issue.
Have a great trip!!