Unfortunately, the upgrades were quite rushed. After you buy an upgrade and remove that part from the clock, it should get replaced by the upgraded one. When you rebuild the clock, the upgrade takes effect.
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I finally figured it out. I would like to say maybe make a small tutorial. I really wanted to like this game, as I did finally find screenshots of a few things in it, and kept seeing it work. Finally realized you could take apart the clock to then replace the old parts. Aside from that one hiccup it looks quite nice. I actually could see this being a full fledged game. Just, maybe make a tutorial showing how to take apart the clock to activate upgrades? Cheers though, a very nice game.