You won't have any problems as long as you have a domain controller still active. I did this a few months ago, promoted one of the bdc's and away it went! I built the server out to sp4, copied the exhange files I needed to the new machine (also used ntbackup on a fresh tape just to be safe). Removed the PDC from the domain, renamed the machine and finished building the server.
Also for recovery purposes I dropped our second BDC so if needed I could bring it back online and use the old mail server if something went wrong.
You won't need the whole directory, basically you need the public, private, and directory .edb's and the log files. I did have to run isinteg -patch before the services would start though. Exchange came back up I had to remove and reinstall the IMS and everything was good. Total downtime was about 2.5 hours.
If you have any more questions let me know. If you can find the book Exchange Server 24/7 page 103 and 104 has the procedure I used. The only problem I really had was forgetting about the ftp directory.