You have done enough, now update.
Notes:
The files you can see in USB storage are specific to your installation of the screensavers.
I.E: Things which you might not want destroyed.
Things on visible USB storage do not effect the update process (other than the chance of them taking up all available space).
The "jailbreak" itself should not effect the update process.
No need to "un-jailbreak" the device before updating.
If everything turns to sh..
There is always Kubrick.