Hey, congrats on being in the final phases of the project!
Keep in mind that learnability is part of user experience design, and that a learning curve is acceptable. Think of a case where small mechanics slowly build up to complete the core mechanic of the game.
Shadowmatic for iOS (http://www.shadowmatic.com/) is a great example. The concept is unfamiliar and hard to process at first, but they walk you through slowly until you reach the full complexity.
Here's my final thoughts (I don't know what your puzzles look like so YMMV) 1) If this puzzle you're polishing builds on previous puzzles, make sure the knowledge gap isn't too big between the previous puzzle and this one 2) If every puzzle is different, make sure that the time needed to figure out the mechanic is appropriate, based on the puzzles beforehand (the same, or slightly longer). If they don't scale linearly like that, let people play out of order and come back. 3) Caution here - be very careful when testing with a user that they don't start doing the right thing, then give up and pursue a wrong second approach. This concept of a user 'exhausting' an approach leads to frustration and giving up, and is a good sign that the puzzle needs more clarity around the direction.
Send me a DM with the game info when it's ready - I'd love to see what it's like