I found some free time for you.
I am on an SMS team aswell. Several of us focus on MSI technology, the repackaging and authoring side. We have a good understanding of how SMS works, and we are authorized to create packages, collections and advertisements, but the real hard core SMS infrastructure design and implementation is left to other members of the team that don't know anything about MSI beyond msiexec /i foo.msi /qn and source resilency.
I would suggest you start by making a "clean" RIS image. For capturing and testing you will need to be able to quickly reset a test machine back to a base state.
The theory is the repackager will see the changes made by an install and save them in the files you mentioned earlier. It will then take those files and build an MSI. In theory the repackager is supposed to be smart enough to capture setup intent while filtering out changes that were made to the OS by other running processes.
In reality a repackager can at best capture only one instance of a setup intent. If the setup would have installed one thing on XP and a different thing on 98 then it will never know that. You have to capture different images for different situations.
IMHO I am not repackager, I am a Reverse Setup Engineer. I use years of experience as a developer to make my self aware of the true intent of an install, and while I use the repackager as my starting point, I end up making lots of improvements to the MSI along with extensive testing before I deploy it..
I hope that makes sense in the context of "repackaging." Please feel free to followup with any questions.