Is JITting performed for each assembly or for each method? How does this affect the working set
In each method. Methods that are not called are not compiled, which reduces the impact on the working set.
This may help: Does the .NET CLR JIT read each method each time?
I agree with Daniel.
If you have access to it, Jeffrey Richter CLR through C # provides an excellent overview of how JIT'ing happens and how the CLR processes the results. This is a clear and concise explanation.