I have an msbuild project which builds a SLN file from visual studio which holds all the projects in (about 70+ project), and a lot of the projects are dependent on each other m
How are you calling MSBuild? If you point MSBuild to the solution file, it should be able to work out the dependencies. If you point it to individual project files, then it won't be able to resolve any project references.
If you don't use project references you can still control the dependency order in a solution by using the "Project Dependencies" dialog to manually set the dependencies.