Cool, thanks for the info and fixes. Regarding the boxes and barrels I walked through, they were located in the northeast corner of the room, to the right of the prisoner cell. It's the one room before the pipe structure/barrier at the end of the walkway on the right hand/eastern side of the pool.
As for the "0" key in the supercomputer room, if that's meant to be disabled that's fine with me; this is your remake that you're making after all. Anything that doesn't fit with your vision of how to remake it, and that isn't a bug, probably doesn't need to be included. The final decision is up to you, I'd say.
Just thought of something else: randomly, in any location, it seems like the player character will sometimes appear to be walking on air, not directly on the floor/ground. I know it's kinda hard to see when it happens given the top-down view, and I haven't noticed any one action or event that causes it, and it goes back to normal eventually, but it's probably something to take note of and see what might be causing that to happen.
Alright, that's it for now. Thanks again!