Is there any rules regarding permanent upgrades? I was very confused as to why I couldn't fly as far or see the thingy with the resistance on the bottom left, and now I realize they're permanent upgrades.

Can you use any/all of those in an attempt?

Yes, using permanent upgrades and things in the bonus shop is allowed. It is recommended you 100% the game before speedrunning it.

It appears I oughta change up my strats. :P