So, I found out how to do this with the Repackager. Here are the directions I wrote up.
Appendix C: Creating an .MSI that has no .EXE
Perform the following to create an MSI when you do not have a .EXE program for installing. An example would be header and library files for a computer compiler program, or you have a software title that isn’t easily monitored.
1. Launch the Repackager utility
a. Start | All Programs | AdminStudio | AdminStudio 2013 Tools | Repackager
2. Select the Tools | Repackaging Wizard menu item.
3. Click the Next button on the Repackaging Wizard window that appears.
4. If prompted by a “Restart Pending” popup, cancel repackaging, reboot your VM and restart the process.
5. Select the Snapshot radio button.
6. Click the Next button.
7. Select the Multiple Steps radio button
a. Select the Analyze the initial system status radio button.
8. Click Next
9. Click Finish
10. Now install your program, create your shortcuts, copy your files etc.
11. When finished with all of your changes you would like captured, launch the repackager utility again.
12. Select the Tools | Repackaging Wizard menu item.
13. Click the Next button on the Repackaging Wizard window that appears.
14. Select the Snapshot radio button.
15. Click the Next button.
16. Select the Multiple Steps radio button
a. Select the Analyze system status changes radio button.
17. Enter Program Name
18. Enter Version
19. Enter Company Name
20. Click more and enter software URL’s if available
21. Enter path to store files : X:\FolderNameForPackage\Project
22. Click Start
23. Click Yes if asking to overwrite the existing project.
24. Click Finish
25. Repackager will open and you can now make you changes before creating your MSI.