Wow, those are some really cool ideas for expanding the game.
I agree that it does currently have a "two-part" game setup, getting the clues then solving the logic puzzle. Technically you could enter the clues you find into your mind castle as you collect them, but while I was testing the game myself, I ended up doing exactly what you describe, getting all the clues first. Even if you were determined to enter them as you go, some clue types require you to wait until you have other clues to do something with them, which would stymie you on that front. I had a few ideas on how to break that up, but ultimately, I had to cut them to keep the scope manageable. But maybe for a future version!
Thanks for playing!