Not to put too fine a point on it, you haven't met our "customers".

Still, we're already at work enhancing our feature to include
automatically modifying the project's "build path" on the user's
specifying the target JRE level, assuming we can get the user to
accurately tell us where the alternate libraries are.

Still, there's no guarantee that they'll do it right, so short of
actually deploying the app to the target and having it blow up, is
there a utility that can examine a jar file (or set of class files)
to match it up with a sample JRE and look for missing method
signatures or classes?

If you can't tell, I'm not really a Java wizard; I just write
Eclipse plugins which happen to be coded in Java.