Some time a go we ran were upgrading a few of our servers from 2003 to 2008. We ran into a few problems with our programs not working properly after the upgrade was finished (SQL was one of them). Fortunately, we were in a situation where we had the time to simply format the servers and start with a fresh install. I don't have any specifics as to what went wrong because of this but I can at least offer some advice:
- BACKUPS!! Make sure you have your current servers backed up as well as all of your SQL files.
- Make sure those backups work!
- Test it out. We weren't lucky enough to have a test environment for this, but if you have one use it.
- Make sure you know the software. A lot of times people will have to upgrade a server but may not be knowledgeable with the software on it. Having someone good with the software can save time in troubleshooting if there are any issues.
- Consider your time factors. What will take longer, doing an upgrade and possibly having to troubleshoot or starting fresh and installing everything?
My advice would be to start fresh. It's what worked the best for us but maybe you'll have more luck.