I was already working on the .capx so didn't get a chance to see your updated file. I think I solved most of your problems, but tell me if I broke something in the process.
WayoftheSax_Edited.capx (r97)
I went with a different approach for both the problems, I used a number variable "currentLevel" to keep track of levels, adding to the variable every time the level is changed.
I also added another variable to trigger a level change. With the "changeLevel" variable, you can do a check if the game is paused every time your layout is about to change.
The layout will restart when you enter/exit the menu, I don't know how to fix that other than not using a different layout for the menu. But at least it should return to the "currentLevel" layout now.
Btw, it's a bit difficult to navigate through your project, you should get used to adding comments (Press Q or RClick) and maybe use some groups.