Failure combining solids due to overlapping edges

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Hello,
I have been working on a project where I have been attempting to fix a library of models of boat hulls to make them "water-tight" for use in CFD. Unfortunately many of the models I am working with are, for lack of a better word, broken. There are a lot of complicated geometries involved created from various lofts and extrudes, and as a result, some of the solids aren't playing well with most of the 3D modeling commands or derive based functions. Many of the commands give me an error such as failed Booleans, and failure to produce meaningful results.
After a lot of confusion, I exported solids individually to STL files, and used the STL check function in 3DS max. As it turns out a lot adjacent faces have overlapping edges, creating a multiple or open edge condition.
I've had some success in converting the solids into surface bodies, and replacing the problem faces with free form faces and creating matched edge conditions (The multiple edge condition makes the patch command a nightmare). However, as I said, there is a lot of complex geometry on the outside of these hulls, and the free form approach isn't 100 % faithful to the original design.
I was wondering if there was any tool in Inventor that can diagnose and check solid bodies and identify problem geometry, and also if anyone has come across a similar problem and has a good fix.