Its awesome that you are still working on it and improving it. Keep it up!
The confusing bit for me was after unlocking the first door, I did not press the scanner, and I just went straight to the main room, picked up the dinosaur and brought it back onto the scanner and pressed the button, and then the skull disappeared and it said "the item is 30 billion years old" and the timer started. To me it felt like it was just telling me about the item I just scanned and did not know what the timer was for. After seeing the skull had re-spawned and repeating this process twice, I figured "oh I am supposed to press the button and then collect what it is describing within the time".
Maybe keeping that main door locked until the player presses the button and the timer has started will help? That is only the first suggestion that comes to mind; there might be better ways to help guide the process.
Anyway, I hope this feedback helps!