This game is weird as to how it allows you to skip already-watched cutscenes. Most cutscenes become skippable if they've been watched and you choose to restart or exit to menu, but they switch back to unskippable once the level is completed. For PC runners, this is worked around as the saves are easy to replace and transfer, but PS3/X360 runners will need to set up a proper NG+ save file manually. Read on if you're playing on console.

First, complete the game as normal, and try to avoid making upgrades you won't need in your runs as they're irreversible. You then need to play through each level again, making sure to activate all in-game cutscenes (or at least the cutscenes in Any% runs), and exiting to menu instead of completing the end of each level. When you're finally done, buy the upgrades needed and keep a backup of your new save, as you'll need to replace it after runs past Something's Amish. You really don't want to lose this.

have fun lol

Also, if you intend to run All Secondary Objectives NG+ (ASO+), your save must not have the final level completed at all, as one of the cutouts in phase 3 always gets destroyed and your save must not have any objectives completed before the run.