Ganners -
Here's GREAT site with step by step for moving an exchange server:
(you'll see on the right column other good links, too, including how to change the service account password.)
Ed Crowley will step you through it and reference a couple of other MS Q articles as well. I'll add one more Q: Q189286 talks about how to del a server from a site.
These steps will get you to a new server (different hardware, which I assume you have since you said "migrate" and not "upgrade" - sorry if this is inaccurate for your purposes.)
On your new hardware, I'd suggest Win 2000 member server (unless you're crunched for hardware, best suggestion is to NOT have exchange running on a NT4 BDC or a W2K DC). You'll want this new server as part of your old domain for the time being until you get everything settled.
As for moving the Exchange server into the Active Directory (AD) - there are lots of possible gottcha's - you're probably going to want to do a lot of reading and/or hire a consultant. The details will revolve around how you move your users to AD - whether you have "SID history" which is dependent upon whether you're W2K native mode. One major issue around this is whether your new users (new SID's) in AD will still have permissions to their Exchange 5.5 mailboxes. If you have only a handful of users, you can manually go and update this "primary NT account" on each mailbox to the new AD user account. Otherwise, you could be in for some headaches.
For your reading/reference purposes, I would suggest this book: "Windows 2000 Active Directory" by Alistair G. Lowe-norris, pub by O'Reilly. It's about $40(US), but well worth it.
Sorry this post won't answer all your inquires, but perhaps it will get you started. Your questions actually involve an entire project scope! Good luck!
aliciaJ