Thank you so much for mentioning this. I did find the solution - it took a lot of searching, but I found it here on the forums.
In order to get combat to work on your independent mod, you must copy the folders ../(unpacked main)/Mods/Main/Story/Alignments to ../Mods/(your mod)/Story
and
(unpacked main)/Public/Main/ActionTemplates to ../Public/(your mod)
After doing this, combat worked! Yay!