I’m about to try the million roses speedrun and I know it’s going to take 12+ hours at the minimum, but do you think it will be okay to pause sometimes for eating?

Sorry, but you will have to leave your timer running if you take a break. With how long the run is, I actually do encourage that you take a break once or twice during this to eat and/or use the restroom, but unfortunately you will have to let the timer run, and just accept the time loss.