I now have aligned bumpers all around!
(SO DIRTY. NEED CAR WASH.)
Turns out there's a sort of locking channel thing that the bumper locks into underneath the well liner. The lower part was hooked in, the upper wasn't, shoving it out and looking bad. Hooked it back in and it looks good as new!
The bumpers were both super easy fixes. The front needed new plastic screw/clip things, the back needed to be replaced in it's proper channel.
Now, if this silicone works and holds my door trim flat on the clip until we can get new trim all around, I'll be supremely happy with the body. It's still not perfect buy a helluva lot better than when we got it. I guess (maybe) I'll peel the roof dip off when it gets warm so it doesn't look as ricey. Then I might be okay with showing it off more.
Oh yeah, we got the coolant filled up. I'm carrying around a half bottle in the trunk now, just in case. When my dad gets his check we're ordering the new pump, so it won't be too long off, probably next week.