Server 2012 and SBS 2003

If you haven't completed migrating everything off the SBS server, move the FSMO roles back to the SBS server and it *should* stop shutting down on you. Just make sure that it's properly replicating. If there's nothing left to migrate, make sure the workstations and devices are all using the new server for DNS and DHCP (shut down DHCP on SBS, enable it on 2012 if it's not already). Then remove it.

To my knowledge all of the roles are moved over. Although it makes me second guess that statement because their internet doesn't work when the old one is shut off.

I would think the secondary (2012) machine would supply their DNS etc..

How do I decommission the old server?

I don't mean to offend, but I'm going to be blunt.  

If this is not your area of expertise, I would suggest creating a gig for this.  If you asked this question before doing all this, I would have recommended hiring a professional to help you, since this is your network and it likely is a seriously important part of how your business runs.  Not knowing what you're doing and feeling your way through the dark after the matter is not a good way to handle this in my opinion.

All the roles are moved over or you wouldn't be having this problem.

Did you update DHCP to provide DNS instead of the old server?

Did you fix the Journal wrap?  Run DCDIAG /E /C /V on BOTH DCs to ensure everything is working properly (there WILL be errors, but some in the expected/appropriate places are fine).

Once you have confirmed things are working properly on BOTH DCs and have finished the task of migrating the rest of the network (DHCP/DNS configs and anything else missed), you can PROPERLY uninstall Exchange from the SBS server so it's removed from Active Directory and then demote the SBS server using DCPROMO.  Skipping steps can leave you with problems today... or tomorrow.  Why this should be done by experienced folks - that experience can come from learning in a test environment too - not saying you couldn't do it, but at this point you have a mess... a potentially serious mess... and the best way to resolve it is with professional assistance (and not just some Q&A on a forum).

You're right Leo, however this is what I was tasked with doing so I don't have a choice of hiring someone to do it.
I did not fix the journal wrap, I will try that tomorrow, as well as verifying that the DNS and DHCP roles are working properly on the new server.

I guess you meant that the roles aren't moved over. I did see entries on the new server in DHCP, but its been a while since i looked in there.

The old server was supplying AD, DNS, DHCP, and faxing service.

I've heard of folks who are tasked with doing something they don't know well.  You will almost certainly be blamed by management for the problems that happen if you proceed.  CYA - explain this is something you are not familiar with and you don't feel comfortable having the entire business ride on your untrained hands.  Had this project NOT begun, I would say to tell them to send you to training.  But since it's already in progress, the answer is hire a pro.  Use a Gig here at EE.  Or consult with experts such as IT Pro Experts or Third Tier.  No, not cheap.  But $500-$1000+ in consulting fees will probably be less than the lost sales/productivity the company incurs from a server that continues shutting down.

That said, you need to fix the Journal Wrap.  Get both DCs working, even if the SBS server is shutting down.  Once you can authenticate to it (which will require adjusting your DHCP configuration/DNS services), you can proceed with the removal of the SBS server.

But I really can't stress enough the importance of a STABLE network and that only comes when things are done properly. And again, I certainly don't mean to insult you, once you take the time to learn it, no doubt you would be fine to do it... but flying at 30,000 feet is no time to start learning to fly a plane...

The new server has the following FSMO roles domain naming master and PDC.
I have all of the computers DNS set to static and to the new server, they can now access network resources when the old one is off.

There are 5 FSMO roles.  https://support.microsoft.com/en-us/help/197132/active-directory-fsmo-roles-in-windows

You still need to move Schema, RID, and Infrastructure.

Here is how to transfer them.  https://www.petri.com/transferring_fsmo_roles

In DHCP you need to change the DNS setting to the new server.  You should not have to statically set the DNS on the workstations.

Once this is done, and as long as there is nothing else on the old server, you SHOULD be good to dcpromo the old machine, then remove it from the environment.  

You will also want to raise the functional levels.

I have DHCP and DNS set up now.
Users can access network files without having static DNS on their computers.

Fixed the journal and got the following as verrification.
"The File Replication Service is no longer preventing the computer AG2 from becoming a domain controller. The system volume has been successfully initialized and the Netlogon service has been notified that the system volume is now ready to be shared as SYSVOL. "

Ag2= New Server

Prior to me fixing the journal the new server status was offline in active directory users and computers.
It is now online.

Edit- Disconnected the old server from the internet to test logging in, as before i fixed journal wrap etc it would not connect network drives etc..
It now works!

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