I think you're right there's a bit of clunk to clean up around the Port Timeout - it's an interesting mechanic that I need to design more puzzles for to get a better feel for - just added to my TODOs :)
I have the same problem, maybe you should set optional goals, like cycles and loc, giving a star, if the goal is meet. I'm sure, most of the players will try to reach the goals. In other games it's common, that you have different solutions to reach the goals.
