Just an update:
Originally got truck back, then took it back in for the headliner swap. 2 days after I got it back, leaking again - but not NEARLY as much water. This time, there was a tiny leak from the roof marker lights, the new gasket they had put on previously was torn (so they say). While it was in the dealer I had them look into the AC taking forever to cool down the air. Turns out they had to replace the AC compressor. Blows ice cold right after start up now, but truck was in the dealer for right at a month. Glad to have it back, but paranoid about issues now.