Hi! I just finished watching the steam video :-).
About the code, basically it is a failure to provide good feedback on my end - the result of making stuff up as i go i guess. Someone wrote that it looks like Tomb Raider - initially i was planning to make a TR-like platformer but making those animations took time and as you noticed, controls are a bit janky... so i just started adding more and more puzzles instead :-P.
Your initial guesses were actually right, it is just that there wasn't any feedback about what to do about the middle number.
Since itch.io doesn't seem to have a way to mark spoilers, i'll give you a hint on what to do: go "at" the book's title (the "at" was intentional :-P) and use the action button. And now i guess you can see what i mean with failing to provide good feedback... there should have been a way to tell when you can interact with something (the same applies with the bookcases - only those in the room are interactive). But i thought of that too late (i made that room near the end of the deadline).
But this is basically a half-baked 3D platforming engine forced to become an adventure game engine mid-development :-P. Anyway, i can tell you the full code if you want, just send me a mail at badsector -at- runtimeterror -dot- com :-).
About some other things. The game didn't crash the first time, from what i can see in ~33:50 when you opened the inventory you had the Quit button highlighted and i guess you pressed Enter or Space which activated it. This is something i pretty much added the last moment (i was killing DOSBox or pressing Alt+F4 for most of the development to exit the game) and the UI system was hacked quickly together in an afternoon, which is why it doesn't have any confirmation popup... or why the note disk text sometimes reads in a weird way (there is no scrolling nor word wrapping so i was trying to fit the text in the few lines and characters as if it was Twitter :-P).
The sound was a bit choppy... my guess is the K6 you use wasn't fast enough. It'll sound counterintuitive but the software version (WINPETRA.EXE) might work better - i've only written the D3D code recently and only tried it on my 1GHz P3 machine whereas i tried the software renderer on weaker machines and optimized it a bit more.
About DOS not having audio and DMA issues: Soundblaster has two DMA types, low DMA and high DMA. The low DMA was there from the beginning but only supports mono audio whereas the high DMA was introduced in SB16 and supports stereo. Post Apocalyptic Petra requires SB16 to do stereo so it uses only the high DMA. Your sound card probably doesn't support the high DMA mode, which is why you get that. There might be a way to get stereo audio out of low DMA-only SB compatible cards because it sounds weird to me that these cards forced DOS games to be mono. Then again, i guess by the time they were new most people used Win9x and DOS support wasn't much of a concern. I might check that out at some point.