The comments below are shots in the dark. I have not read your prior book and really don't know your characters well enough to say, "Oh! With this guy's weakness, you could do such and such to so and so and allude to this." Hopefully, it helps generate more ideas for you or is at least somewhat beneficial!

Domici wrote:
There are several themes I'm looking to include as background material in my next NaNo story. Missional Living, Children being loved, and strong friendships. Please read the rough outline of the story (Tween Christian Sci-Fi) below and suggest other aspects of theology I can hint at or allude to.
Just within "missional living, children being loved, and strong friendships," you can allude to many many little aspects of theology. (See below)
Domici wrote:
... Wilbur and Gray are becoming friends but the audience is tween...
You could display the power of forgiveness here if it were so written.
Domici wrote:
...his mom works three jobs to support four kids, and his older sister just started working at the local grocery store...
...“Thank you Mister Lefron.” Akil was following clues to this particular slave, who is Wilbur’s dad...
Just the fact that mom is working so much shows
storge quite well (or it would seem so).
I don't know what happens to Mister Lefron after the pirate ship is claimed by Al, but love for children, here, definitely. xD He could have the chance to be with his child again! (I know.. not a new idea to go with, but I was excited) Is there potential to showing respect for parents (and all that surrounds that)?
Domici wrote:
...Akil (M) is one of the older brothers Al found out she had last book...
Here is potential to show
philia (Not that they are brothers, but it is close..., the exhortation of one sibling for the benefit of the one exhorted, forgiveness... et cetera.