Windows Server SBS 2003 to Server 2012 R2 Migration advice

You seem to be at the point where you can decommission the SBS server. An SBS server requires that it holds all the FSMO roles, there is a maximum of a 30 day period but there are issues involved. Once you transfer the roles you should remove the server from your environment.
>> http://www.sbsmigration.com/  << a very helpful site

I haven't worked with SBS before. From what i gathered the steps are

Move FSMO roles to DC01
metadata Clean up
Why?  Are you NOT planning on properly demoting the machine?  If you properly demote the machine, there is no need for a metadata cleanup.

Stop Dirsync
Why?  Are you using Office 365?  What is DirSync if not a component of Office 365 (I've not had an SBS 2003 box running for a while now, but I'm fairly certain having worked with the product for years that it wasn't a component of SBS 2003.

Remove Exchange
Correct.  You want to remove Exchange.

Repopulate Mail and SMTP attributes (Found a neat PS script for that)

Again, I assume Office 365?

Start  DirSync
Office 365?

You really should be more verbose - you said "From what i gathered" - where did you gather it from?

Demote SBS01
This should be done before removing it and AFTER you have removed Exchange properly.

It looks pretty straight forward but i saw a few posts where as soon as they moved the FSMO roles, Domain started having sysvol issues and replication issues
You SHOULD be shutting down the server BEFORE you demote so you can simulate not having it on the network.  You should also be running DCDIAG BEFORE modifying anything else in AD and confirm the health of AD - I usually run DCDIAG /C /E /V on EACH DC and then confirm everything passed - things that don't pass, I research until I'm satisfied it's not an issue.

Any ideas or tips to avoid this kind of a disaster?
Get experience doing it before doing it to a production network.  Setup a test network and do this two or three times until you've gotten most of the common issues resolved and understood.  Learning on a production network is unwise at best.  If you don't know/haven't done something like this before, then you would be wise to hire a professional who has.  Just like no doctor has seen every scenario of medical issue, no consultant has seen every scenario of upgrade/migration issue on AD, but with EXPERIENCE comes increased success and less likelihood of utter failure/disaster.

Migration went through without a hitch. Didn't need a meta data clean up .

You need to clear all exchange attributes from the system manager on 2003 box before you uninstall exchange and you need to login as the SBS built in  administrator (We had the default admin account disabled)