The factory pickup screen has a trap door that will let some pretty big stuff past it. Any idea if you're still running one of those?
also, have you examined the filter adaptor CLOSELY yet? push on the pointed filter bypass just above the filter threads and take the relief spring and valve out and look down in there. I guess there's a small chance one of those parts came loose and got routed into the pump.
Since every corner was chipped off I can't help but think something hard was hanging out in that area beating the crap out of them for a while. What does the other gear and the gear pocket look like?