Hi
This is a big job, and the simplest method to do this is a mini re-implementation,
What you should do is to create a new blank database, you could also do it a a separate company in the database however if you are doing this rather start with a fresh database
Use the Rapid start services module in 2013, or Data Migration in 2009 to export all the master records (Cust, Vend, GL, Item, etc)
You can then update them and import into the new database
From there you will need to get either transactions or open entries to the new system, we try to load only open entries as it makes for a clean system but this depends from site to site
You can use the method to bring in these transactions or a Data / XML Port, the ports are a lot faster so if you have 100k+ transaction you possibly want to use the ports or you will have to spend a lot of time waiting for imports
Shout if you decide to go this route and have any other questions
Cheers
Nev