"Of course there are some DLL problems and there is a lot of custom code involved."
This is you're issue then. If you don't upgrade your external class libraries to point to the new DLLs (remove the references and re-add) then when you build them, it will put in the OLD DLLs, and thus replace the proper libraries.
Sorry, but no way around it, you need to rebuild those other class libraries using the updated dlls, otherwise you're going to create more problems than you can diagnose.
Keep in mind if you can't find the source for your custom libraries, JustDecompile is a free tool that you can hopefully salvage your custom library classes and rebuild them. I know i've run into it before where other parties created libraries and didn't give the customer the source.