RE: Merging two companies that already exist in MS Dynamics GP 2013
Sarah, the process is a bit more complex than you might consider at first pass. The issue when combining data is that you can not simply smash the two ( same name ) tables together - especially as you noted that they have same GL, the same payments, similar vendors.
When that happens, you are way more likely to run into duplicate keys all over the place.
Like you I like to try to do my own work, but when it comes to this, I would reach out to an organization like CRG and get their assistance. When you use this type of service, you reduce the risk that you are going to encounter when doing this type of work.
I think this is a time where safe vs sorry has a cost, but I think cost is worth it for this.
Hope this helps.