Jay, one of the challenges with the MR migration is that when you run the migration the process destroys the content of the MR side - each time.
As I recall you can migrate unlimited company details, but you an only migrate really one spec-set at a time.
We had a similar problem, two companies, two spec sets, but only one MR.
So, we migrated one - completed successful testing.
Then in MR we exported the data to a 'backup'
Then we did the second company migration and it was completed sucessfully.
At that point, we imported the first company information back into MR - set up a FOLDER for the reports to keep them separate and we were off and running.
We applied the required security to keep the two databases separate as needed and have not had any issues since.
Hope this helps.