Hi LKHarris, that’s quite and handful you have there!
Let us take a step back and review the situation somewhat. You are looking to transition or migrate and consolidate from seven domains, one Exchange 2003 Organization and five Exchange 5.5 Organizations into a single domain forest and Exchange 2003 Organization functioning in Windows 2003 and Native mode respectively. You would also like step-by-step instructions on how to accomplish this.
Essentially, what you are asking for is consulting services. There are a number of things for which step-by-step instructions can be provided, such as how to raise the domain and forest functional level and Exchange operating mode, but it is not practical to provide the same for your entire migration because the “cook book” would have to be specific to your environment, as opposed to a vacuum scenario. There are simply too many variables to consider.
Do you plan on migrating into the existing root domain and forest, or a new forest? This decision has implications on what methods and tools can be used to migrate users and data.
You will also need to do due diligence on planning and designing the target Exchange 2003 Organization to support all of the users (see: Here).
Since you are using Exchange already, it will be relatively straight-forward to obtain mail statistics using something like Quest MessageStates or a similar tool. You can use MessageStats on a trial basis to gather your statitics; however, it is also a useful tool to have for the proactive monitoring and management of the environment on an on going basis, for which you will have to pay for and properly license, of course.
My immediate advice to you, is not to do anything. That is, freeze the existing environment until you have made some initial decisions and even then, do not perform any unnecessary upgrades. You want to pursue the path of least administrative overhead. To summarize that thought, if you are migrating into the existing root domain and forest, I would not pursue raising the functional levels and operational mode until after the migrations are complete. On the other hand, if you are migrating into a new domain and forest, then I would raise the functional levels and operational mode following installation, prior to performing any migrations.
This isn’t exactly a “You’ve got questions. We’ve got answer.” (RadioShack) scenario, but if you need further guidance, feel free to ask more questions.