Hi Melissa
I didn't see your post right away and hope I can still help somewhat.
As I've mentioned before, I'm in Kingston quite a bit and I find it an amazing city to visit.
You've already chosen some good places to visit. Along with the Bob Marley Museum and the National Gallery, you should visit Devon House and the Peter Tosh Museum...all are located near your hotel.
Port Royal is an interesting history tour and I recommend having a meal at Gloria's right in Port Royal...very charming and unique town.
If you only have a couple of days, I would choose either Blue Mountains or Hellshire Beach as you may not have time for both. Since you've seen the more beautiful beaches in Jamaica, maybe check out the gorgeous Blue Mountains instead...Strawberry Hill is expensive to overnight, but it's relatively reasonable to enjoy a meal there.
Dub Club is only open on Sunday evenings but you can also check into Skyline....which is open Saturdays and almost next door...both are an enjoyable experience.

If you need anything further or more detail, feel free to ask.