Hi Steve, thanks for posting!
I'm afraid that NCrunch wasn't designed to be able to deal with heavily customised builds such as this. The features it provides exist basically through close manipulation of the build process, so there are certain assumptions that it makes about build operation (such as a single project emitting a single assembly file). You may find it impossible to get NCrunch to work with this kind of project without making large changes to the way your build system works.
When NCrunch executes a build, it interrogates MSBuild for the name of the assembly output from this build. The property combination it uses to find this assembly is $(OutDir)$(TargetName)$(TargetExt) .. Should the assembly not be found using these properties, NCrunch will revert to 'best effort' mode where it attempts to find the assembly using a wide range of different possible combinations, all of which are based off the $(AssemblyName) value.
If you're able to adjust the batch files to align the output assembly name with the above search logic, NCrunch should be able to locate the assembly. However, you'll still need to split the projects so they only output one file each. As it sounds like your build process was built manually from scratch, I'm also not sure whether you may encounter further issues beyond this as NCrunch has only seen extensive testing around normal build processes built using the Visual Studio templates.