The clues were too difficult, or non-existent such as with the swords. There really wasnt any way to actually figure out to work that pattern. I know that they made sense to you since you wrote the game, but you need to consider your audience when making these.
The worst part would be the math thats involved in figuring out the code to the door. Actually having to sit down and figure out that puzzle and then figure out an equation is time consuming which is obviously a constraint since your score drops every second you spend in the game. I would find another way to score the time rather than a countdown. Especially since you have such a difficult game to figure out. There also needs to be some kind of explaination of the items you find...vague sure...but the character your playing would have some idea of the item he/she found...despite how cryptic. The lock picking tool wasnt really obvious, the reason for the rope wasnt clear enough to figure out without some kind of clue about the gears in the cabinet, which looked more like plates of some kind rather than pulleys or gears.
Ultimately I had to use the walk-through to finish the game and I started using it rather early. A walkthrough shouldnt be needed to finish the game but rather to get past a sticking point.
Just remember that it makes sense to you because you made it, players arent going to have the same insight to the game that you do.