Heyyy, thanks guys!
Okay, okay, the picture is becoming clearer; I'm narrowing down on what I need to ask, LOL.
You can get mutant alliance tokens from a few different things. If you're not getting the humanist safehouse or alliance traitor missions you can still get tokens by freeing mutants from a few missions, like the academy outpost or the ghoul town missions. Upgrading the bounty level gives more opportunities as well. The RNG can be a bitch sometimes, especially when you're looking for tokens. The current game I'm running I had to buy a ton of Zaxx tokens which I really don't like doing but the game was being a jerk.
I've been rescuing Alliance members when I can, and I'd considered buying the tokens outright, but I didn't know if tokens alone would lead to "Alliance Favors", or whatever. Maybe upgrading the bounty level will help shake up the variety of the missions offered, 'cause I'm still on D, haha - and it's good to know that my game's not broken, it could just be crappy luck that I'm not interacting more with the Alliance. Thanks for the the info, @Zippicus!
You can still shoot something down relying on visual identification of UFOs. Interrogating prisoners unlocks the Bootypedia entries and all the pictures are in there.
The Sci Books necessary for the Library can also be unlocked by doing a prison raid in the Dr. X arc. You'll need an Academy Esper for that, but if the RNG hates you, you might get one before an Assassination Trophy.
Yah, I just started doing visual assessments, lol - I remembered that there was a contraindication, blue and red lights, but I couldn't remember whether they meant Attack or Do Not Attack, haha. Sometimes it can feel like a slog going back into the 'Pedia for little bits of critical game info, but I'm not complaining about a lack of content, that's for sure.
So, whether I run into Espers or not (I haven't), and whether I get lucky with Alliance and Zaxx missions (I haven't), it sounds like all I can do is upgrade my bounty level one way or another and wait, amiright? Thanks again for all the helpful replies, a little assistance goes a long way!