I have worked out most of the problems I was having with EasyTuTu and the various tweak/fixpacks I was having and have been playing through TuTu with the Indira and Finch NPC mods installed(and both in my party).

Questions and minor **SPOILERS** below:

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I finally managed to find all six of the library books Finch needed for her quest and talked to the guy in Nashkel Manor. Everything went fine and the library was set up & I got my exp/reward.
But when I checked her bookbag in inventory she still has two of the books(Joy of Pudding and Calimshan's something-or-other.).

What do I do with these? Sell them? Is this a bug?

I think this is just a bug. As best as I can recall, all the books dissapeared when the quest was complete. The setting up the library IS the end of Finch's quest so I say just sell them.