As promised, here's the completed print.  I'm really happy with how this turned out.  You can download the files here...
https://www.thingiverse.com/thing:2687193
For some reason, I can't add photos.  It's only allowing me 60kb?!?  Oh well, just click the link and you'll see pictures.
 
 

Hello all...
I have some pretty rudimentary 3D design skills, a 3D printer and probably a little bit of OCD when it comes to board game storage.  I thought it would be cool to have a little case for the hex tiles.  The 3D printer is running right now and should finish in several hours.  Here's hoping I got the measurements right!  The smaller part is a lid.  It's upside down in the picture.

A binder is actually a really solid idea.  This one would work great.  It holds 160 cards.  There are 159 numbered cards in the stack.  Simply keep the "starter"/starred cards separately.  I think I have one of these lying around somewhere.  I might use it for Fallout.
https://www.amazon.com/Ultra-Pro-PRO-Binder-4-Pocket-Black/dp/B0094J1PJ8/ref=sr_1_2?ie=UTF8&qid=1512480415&sr=8-2&keywords=ultra+pro+binder

Yes!  We ran into the same issues when playing the Far Harbor scenario.
 
Regarding your first issue - eventually there is an encounter card added to one of the decks (settlement I think?) that allows a player to purposely place a shield at their current location.  I still agree this is confusing and unclear what should happen when a shield is placed due to activation.  Would *love* an official ruling from FF on how to resolve. (Until then we are going to play with only the explicit encounter-based turn-in).
 
We also had 6-8 active quests by the end.  It slowed things down a bit because everyone had to review them when deciding how to spend their turn.  However, it didn't ruin the game for us and it feels consistent with the Fallout video game experience, where one can easily have a ton of active quests available at a time.
 
Also, all 4 scenarios in one day?  Nice :-)

I emailed the designer this exact same question, I'll post back here when I get a reply