FatDog,
As some of the replies indicate, this is a terribly hard problem to solve with an automatic one-size-fits-all approach. Since you are doing cleanup, it is unlikely that the code has an extensive test suite. If that were the case, it would be possible through trial and error to comment out each module and see if the comprehensive test suite still passed.

Depending on the size and the complexity of the code and the amount of time your boss is willing to let you spend refactoring, you might just want to start from scratch with each one in turn. Examine the code of the prior code, write tests, write code, check tests, bugfix as necessary, document - wash-rinse-repeat.