I've contacted Benchmade's warranty department after having stripped the pivot screw (trying to break the Loctite) and one of the handle screws on one of my Grips. They sent me a full set of replacement screws for the knife.
If the screws are still stuck, you can try to cut a slot in them using Dremel, and then use a flat-head screwdriver to get it out. If the Loctite is still intact, you can also try applying a little heat (using something like a soldering iron) to soften it up. Unfortunately, the screw extractors kits all seem to be too big to fit any of the handle screws (I've tried a couple different sets that looked like they might be small enough). Sometimes saturating it with WD-40 can also help get it un-stuck.
As for general re-assembly tips... Put a piece of tape over the blade edge (to avoid accidental cuts). I use the stem from a Q-tip to hold the Axis lock open when re-assembling (a bit thicker than a toothpick, and it gets the Axis lock out of the way a little better). I also use a toothpick to help thread the pivot tube back through the handle scales, liner, washers, and blade. It can be handy to help make slight adjustments to the washers if they slide around a little. When tightening the handle screws, don't over-tighten. They should be snug, and you'll want to use some Loctite to keep them from slipping. That was one of my main frustrations when trying to get the blade centered. Thought it was pivot-related, but it actually turned out to be the handle screws at the base of the handle.
