Hmm. . . I deleted all my masks and built them from scratch. . . and now everything appears to be working. My new clipping mask is no longer clipping everything above it.
One thing I noticed that I didn't see before was this handy field, End slot:
Even though my handy 'scissor icons' aren't showing up (is this a bug? it feels like a bug), I can still see where the mask is supposed to be ending, which was crazy-helpful for troubleshooting. : ) I can't believe I missed that handy little field before.
Still though, I do sorely miss my handy scissor icons, and I miss seeing things affected by clipping masks being highlighted in red in the Draw Order section.
But regardless, everything is working the way it should now, so I'm a happy camper! Just wanted to do a follow-up post incase this helps anyone in the future.