Asking these questions means you should probably learn a lot more before attempting this work as it has the potential to create a great deal of down-time.
1. It is not best-practice to make your Active Directory Domain Controllers file servers. Yeah; I know they host a special SYSVOL share... but it is not good to have it doing other tasks.
2. Avoid Server 2008 Standard and go with Server 2008 R2 Standard unless you can't run 64-bit in which case, you wouldn't be able to run Server 2008 R2.
3. Never used KIXSTART, but that seems crazy to me as it is NOT an industry standard. I would personally ONLY use VB Script (i.e. wscript) or now PowerShell. This doesn't mean there is anything wrong with KIXSTART though... just that I don't know enough about it to help you, and I currently have no interest in finding out more about it.
** If you can tell me exactly what this script does, I could probably find you a comparable VBScript to do the exact same thing.
4. Active Directory is (easy peasey... piece of cake)... DO take a System-State backup, but you will not need it if you do things right.

Whatever you do, DO NOT Backup/Restore it! Instead, just
1.) Install Server 2008 R2
2.) Set a Static IP Address (in the proper subnet,
OUTSIDE the DHCP Scopes)
Obviously, you should set: IP, Subnet Mask, Gateway, DNS1, DNS2..., & the DNS Suffix, too! You had best select "Register this connection's addresses in DNS" This will probably happen when you join the domain anyway.

3.) Pre-stage the computer object for it in DOMAIN\Domain Controllers (optional)... then join it to the Active Directory domain as a member server.
4.) Verify the Object by ensuring the OS fields and DNS Name populated indicating both the server & Active Directory agree this new server has joined the domain.
5.) If you didn't pre-stage the object, then move the object from DOMAIN\Computers to DOMAIN\Domain Controllers
6.) Check your existing DNS server(s) to ensure they are using Active Directory Integrated Zones... If not, migrate the zones.
7.) Check that the reverse zones are setup and working too! i.e. nslookup [ip_address] should give you the name.
8.) Look in Active Directory Site's and Services to verify the Active Directory SITE the current Domain Controller(s) is/are in. I.e. Make Certain the IP Address sub-nets are configured correctly for the current network, so the computers know which Domain Controller(s) are close. Make sure you don't have any broken/abandoned Domain Controllers while you are in there.... if you do, clean them up.
9. From a Client Computer in the Domain, or your just added member server, at the command prompt type: c:\blah blah blah>
set L It will display LOGONSERVER=\\SERVERNAME That should be a Domain Controller in the current Active Directory Site.
You can make a VB Script like this (saved as a .vbs):
Code:
Set objADSysInfo = CreateObject("ADSystemInfo")
WScript.echo objADSysInfo.SiteName
It WILL display the Active Directory SITENAME the server is in. Obviously, it has best be in a SITE that the Domain Controller(s) on the local LAN service.
If it is all screwed up, you could be authenticating against a Domain Controller on the other side of the world instead of the one 5 feet away in the same room!
10. Check Replication with REPLMON
**** If you have ANY problems with Active Directory, fix them with ntdsutil before proceeding. If you have any Domain Controllers that were not properly demoted or failed, this utility MUST be used clean up any broken domain controllers to remove all their links and connections... (until you get to 2008 where this functionality for deleting failed Domain Controllers is built in)
Make sure you have the Latest Service Pack installed (also on all pre-exiting Domain Controllers). You should run Windows/Microsoft Update, too!
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11. Install Active Directory on the new, Member Server.
DO NOT take Active Directory off the current, running Domain Controller Yet! or you WILL have a very angry customer!!!
** Terminology: Once you Install Active Directory, your Member Server now is called a Domain Controller. It is no longer serving the role of Member Server.
Installation of Active Directory:
12. You want to select "An additional Domain Controller for an existing Domain." DO NOT select "Domain Controller for New Domain"...Your customer doesn't want a new domain, child domain, or a new forest.
13. Now, you enter the username, password, and domain of someone who has enough rights to install a Domain Controller. Obviously, this person must be a Domain Admin. If you were doing something else like creating a new Domain, you would need to be an Enterprise Admin.

*If it says wrong password, that is obvious. If it says "The Domain Controller Cannot be Contacted" you typed the domain wrong. Another possibility is that it could not locate an SRV record for _ldap._tcp.dc._msdcs.customerdomain.com. You MUST specify DNS servers that host Active Directory Integrated Zones when configuring the network adapter above... A caching DNS server i.e. Cisco ASA firewall would NOT have the appropriate SRV records, so this would fail.
14. Now, you are going to be asked to browse for the Domain... Yeah; I know you just typed it... but click browse and click it with a your mouse.
15. Do NOT change the Database or Logs folder where it will install the Active Directory Database... it will usually default to C:\WINDOWS\SYSVOL (Perfect)
16. Confirm the location of SYSVOL and DO NOT even think about messing with its rights, or share settings if you want Active Directory Replication to work. I.e. Just click Next (don't touch anything and you will be fine).
17. Set the Active Directory Restore Password...
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18. Verification... Verify ntds.dit was created in the C:\Windows\SYSVOL folder on the Domain Controller.
19. Verify the NETLOGON & SYSVOL shares exist on the Domain Controller
20. Verify the presence of the SRV records, so it is discoverable by client computers.
21. Open Active Directory Sites and Services and make sure this Domain Controller IS in the proper SITE & that it has NTDS Settings.
22. Make sure you check "Global Catalog" if you actually want this Domain Controller to have its own copy of the Active Directory Database.
23. Check Replication with REPLMON (the Active Directory Replication Monitor). You can force replication right in Active Directory Sites and Services by Right-Clicking on the NTDS Settings of the newly promoted Domain Controller and selecting "Replicate Now."
24. Now, Open Active Directory Users and Computers and specifically connect the console to your other Domain Controller. It should show ALL the objects. Any changes you make to either Domain Controller should replicate to all other Domain Controllers in the Domain. You can simply connect to another one and keep refreshing then checking the properties of an object you change if you want. Eventually, you WILL see your change.
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DO NOT DEMOTE or REMOVE the EXISTING DOMAIN CONTROLLER(s) YET
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25 Where are the computers getting their DNS servers from? If that is the ONLY DNS server, you would really mess up the network.
26. You can easily setup your new Domain Controller as a DNS server... just check the DNS box and tell it to use an Active Directory Integrated Zone... It should automatically replicate ALL the DNS information from the other DNS servers.
27. Okay, so you have at least two (2) DNS servers... If not, you made your new server a DNS server... Great!
How will the work stations know?
A: You must configure DHCP to push out your other DNS server(s). If it is only pushing one (1) DNS server IP address to the workstations, then you take down that DNS server... they are going to hate you when everything quits working! Simply put, setup DHCP to push out your new server's DNS info...
28. At a client/workstation IPCONFIG /RELEASE then IPCONFIG /RENEW... (maybe just the renew). It had better pickup the IP Address of your other DNS server and show that when you do IPCONFIG /ALL
29. Verify NSLOOKUP queries to the new DNS server(s) work. If the computers can't find DNS, nothing will work.
Note: You really should have the box checked for Dynamic DNS, so DHCP updates DNS with each computer's IP address and DNS Name automatically & dynamically! You should probably also setup DNS Scavenging.
30. Where is your DHCP server? If you take down the existing Domain Controller and it provided DHCP... As soon as you leave and they reboot a computer they will all start getting 169.254... auto_ip addresses and not work for anything! If this is your DHCP server... You will need to set that up on another server and check the DHCP scopes...
31. Now, if you want to take down the Other Domain Controller, you MUST make sure it is not hosting any Operations Masters (i.e. FSMO roles). You can run c:\> netdom query fsmo.
It will tell you which domain controller hosts the PDC Emulator Role (needed for time sync, to logon, by Kerberos, for security, etc.); it will tell you which Domain Controller hosts the RID Master (Needed to create groups etc. This is responsible for assigning GUIDs to objects... Without it, you won't be able to create things like groups!). It will tell you which server hosts the Domain Naming Master (needed to add/remove Domain Controllers and/or Domains)... The Infrastructure Master compares objects... This should actually reside on a Domain Controller that doesn't have a Global Catalog unless ALL Domain Controllers have a Global Catalog. The Schema Master is needed to extend schema... etc.
The point I am making is that there are Operations Masters on the old Domain Controller, you MUST transfer them before removing the old Domain Controller! (yeah, you can SEIZE the masters, but you don't want to have to do that emergency procedure)...
Just read this:
http://support.microsoft.com/kb/324801
Now that your original Domain Controller server is not needed to do DHCP, it is not the only locatable DNS server, it is not the only server with a Global Catalog, it does not have ANY Operations Masters, you can remove it. BUT DON'T JUST YANK IT.
You must remove Active Directory Domain Services from it.. I.e. Start > Run > DCPROMO on the 2003 box and tell it you wish to Uninstall Active Directory. It will remove its mess from LDAP, DNS etc... and tidy up.
Before you do this, shut it down and make sure EVERYTHING works!
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Now that you succeeded in replacing the Active Directory Domain Controller with No Downtime or Hickups:
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Your new 2008 R2 Domain Controller is STILL running in Mixed-Mode with a 2003 Function Level.
In Active Directory Users and Computers, do a search for ALL Domain Controllers! Make sure they are ALL running the SAME OS i.e. Server 2008 R2.
Raise the function Level from 2003 to 2008 Function Level... Change it to operate in Native Mode.
After you do this, you will NEVER be able to add another 2003 Domain Controller to this domain again! But you get the new, fancy features.