I don't know if my "Judge Feedback" is actually visible to you so I just want to say here that whilst your game obviously had some drawbacks, it really was fun, so you've already got the most important ingredient sorted!
If you learned a lot from it, I would hardly call it a failure. ;-)
What helped me in terms of keeping track of puzzle design and (even more importantly) game flow was using simple flow charts to keep track of puzzle dependencies. Draw.io is usable directly in Gdrive and I find it really good for this sort of thing, if you want to give that a go.
Looking forward to your future games!