I would go with Livesplit. It's easy to use and you can customize it pretty easily. I also uploaded a preset of splits for the Intro category in resources. That's my personal preference though. There is also automatic splitting for Livesplit, so you just have to start and stop the timer and Livesplit will automatically take your splits for you.

What settings should I use that will optimize time? I know be in offline mode to remove submission of score but what else?

So I just started to speedrun this game and I went into options to turn off Submitting scores and I did and it still submits them. Am I doing something wrong?