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.

i believe it was because I set the disc speed to be fast for PS1 on my PS2 settings. I think that alone saves the multiple minutes.

Any controller you feel comfortable with for mashing buttons. Runners have used many different game console controllers, keyboard, and even fightsticks. Some runners swap controllers during certain levels, such as plane levels. It is entirely preference. Any use of turbo/automatic inputs are banned.