Not an easy task, but I admire your ambitions. Actually, we did the same thing a couple years ago, but also were dealing with the other division/location using a separate UNIX based ERP system. We were duplicating transactions into a separate company into DBA, making for a lot of extra work and overhead. Got them running DBA over a VPN before moving in, which helped the transition.
 
Copying their files to their respective folder as you have mentioned is all you should have to do, after setting up each company on your base installation of course. In the end, we combined our "companies," which was another task all by itself, but all worked well once complete.
 
The way that it was decided to accomplish this was to set up a purchase order for all of the inventory from the company moving in to transfer into the default company. Wish we had the enhancement that allowed for larger purchase orders at the time, or rather our bookkeeper, as we had to create multiple orders due to line restrictions.
 
HTH!

If you want to actually merge the data of the companies later on contact Lynn directly and spend the money for a custom program to do that. I think she created one for another client some time back that might be able to be dredged up and used with some possible updating.