Is there a way to use the toolkit to set up Rocksmith to skip all intro screens?

You don't need to as it's already available here: http://bit.ly/RSMods under the "Older mod methods/low wait intro files/with loft" folder. In there you just grab the cache.psarc and replace it with the one in your Rocksmith folder. Make sure your drive is an SSD as it requires a high speed drive to boot the game fast.

the link you posted is dead

Yeah, I'd appreciate this too!

This one should work (for now) http://rocksmith.rocks/mods

Thank you!