Well let me just reiterate that for the most part it was pretty well done - especially for a first game!
I might be a bit out-of-date on game references as I caught a couple more obvious ones, but didn't really notice that many. So maybe level 40 would make more sense as a reference, but I stand by my claim (which it sounds like you agree with) that's it does rather break the flow.
As for the moving blocks themselves, I understand wanting to keep the game interesting, and there's nothing inherently wrong with moving blocks and timing puzzles. I think what makes it "feel bad" (to me at least) is that it's a fairly sudden change to the game. Up until that point it's all up to the player to figure out the patterns to move in to solve the puzzle, and then suddenly there's timing puzzles and the game is setting the pace (which then level 40 takes to an extreme). Don't know if introducing the moving blocks sooner so the player doesn't get into a particular mindset would help, or if it's just the way it is. But that's just my armchair analysis of why the moving blocks bugged me (although I'm certain a lot of my irritation with them was retroactive from L40 😆)
But keep up the good work!