I gotta agree with this one. 55k LOC really isn't that much. If you have a duplication problem, you probably have a factoring problem.
Refactoring the code will not only help eliminate your duplication issue, but will also teach you what the code is doing, and result in a much better end result than simply eliminating duplication.
Eliminating the trivial copy/pastes is a good start though, anything that helps maintainability will buy time for refactoring, helping others avoid making the problem worse while you race to make it better.