Simple, take FRF offline for a hour or two and upgrade to v4. Trying to do it while the site is still accessing the database is a nightmare. Same thing goes for the merger. Pick a date and let all members know the sites will be down during the merger.
Yep, I know that may be the only way. The deal is that, I do not like 4.0 yet. I still enjoy 3.x much more then 4.x and I would also have to reskin/redesign the forum and that will take another few weeks to do too. I am still looking into seeing if it can be done with the setup I have now, but I know may in the end have to update FRF. We will see.