I'd plan on disusing one of the Active Directory forests and trashing it. Maintaining a multi-domain, let alone a multi-forest, Active Directory is just a pain.
If you don't have a large number of users / computers or complex filesystem permissions in the forest being disused I wouldn't even bother with a tool like the Active Directory Migration Tool.
Migration tools are fine for getting something done quickly, but if you have the time to setup a trust relationship between the forests and move deliberately you can give all the file permissions, applications, and any other services that rely on Active Directory a true top-to-bottom review and assimilate the acquired company into your Active Directory in a controlled and coordinated manner, instead of bringing over a lot of baggage from their AD that'll turn out to be a "legacy" millstone about your neck for years to come.
I'd setup a trust relationship between the forests such that users from one domain can logon to computers in the other. Then, the domain membership of the client computers becomes somewhat irrelevant. I'd deploy a number of domain controllers for the destination domain into the acquired company's office. You could even deploy these as VMs on the existing domain controllers, Windows licensing nonwithstanding.
I'd map out what Group Policy is being used for in the forest being disused, and stage sites and OUs in the destination forest to house the computers as you move them over. You'll probably find that they're not really using Group Policy for much of anything (seems, depressingly, to still be the case 9 years after Active Directory and Group Policy came onto the scene), but definitely give it some thought.
I'd deploy a startup script using the "NETDOM" tool (see http://technet.microsoft.com/en-us/library/cc781853(WS.10).aspx) to disjoin the client computers from the forest being disused and join them up to the destination forest. User logons will continue to work as they always have for the users of the forest being disused.
Whether or not to migrate the users and groups from the forest being disused would depend on the number of users and groups and the difficulty of just re-creating the users, groups, and filesystem ACLs in the destination forest.
You didn't mention Exchange. If Exchange is in play you have cross-forest / cross-organization mailbox migration to worry about. I'll refrain from comment on that issue unless you update and say you need information about it.