The Benchmarker and Waymarker badges are about other games (Benchmarking and Waymarking) that are created by Groundspeak but which are not geocaching. Thus, they are not included in Project-GC's version of BadgeGen.
Lost & Found events were events held during a short period around geocaching's 10th anniversary. If you didn't visit one then you have no way of doing so later. (In my opinion, it was a bad idea to make them a special cache type to begin with; that kind of thing is much better done as a souvenir.)