I went through and fixed a bunch of stuff you mentioned. Still on the hunt for those boxes and barrels you walked through.
The "!" showing up late was happening on one hit kills because the kill happens so fast the code is late firing. I think I have it fixed now.
I enlarged the blockers around the sludge/sewage pools so the player can't get over them no matter what now. Also I re-enabled the cheats for the endgame bosses, and fixed the player still being under control during those cut scenes. Pressing buttons during the cut scene must have broke the code or something. All controls are now disabled during the cinematic now, and it should fix the black screen as well.
Thanks for reaching out with your finds. Cheers!