First there's a bit of a difference between the generic word Paint and Alumahyde II. I'm a bit less concerned after reading the whole post.
The little orange moldable ear plugs work great for plugging the muzzle. (J.E. Custom pointer)
If it were me doing it I'd "paint" everything visible with the bolt inserted. That is I'd paint the bolt but not the lugs. I'd paint the outside of the action after having removed the trigger. I'd fill the chamber right out to the front of the magazine and mask off any bearing surfaces and the left inside of the action.
I'd remove the bolt innards prior to painting also.
Go here: A Good Coating Choice??
Also see "Similar Threads" at the bottom of your screen
Give it a go and show us a pic. We need more reports on durability etc.