Unless you're doing something "non-standard" there should be no reason why any reference won't continue to work after a clone on the new drive. References are based on the root mount point "/" which relates to the root of the boot drive so regardless of the boot drive the references will remain to work.
Unfortunately some companies, Native instruments being one hard code the volume into their setup files which is really annoying.
Is there any way of getting spotlight or finder to search for all plist files containing a certain string? It doesn't seem to work for me is it because they are system files or something?
Quicken Data files are actually packages, which can contain alias to the volume. Once I stripped the aliases from the data file, no problems, but for the longest time (years) everytime I cloned and used a different volume I'd run into trouble.
LittleSnitch hard codes the volume name, but also WHERE on the volume, an application is located. Very annoying.
So it may be plist or preference, but it could also be writing an alias to data file, or even back to the application package itself.
You would think at some point during testing especially, a light bulb would go off and realize there is a better way to code (unless it really is deliberate and trying to tie a program to only a single volume type system, which the Mac doesn't need to be).
Feedback the vendor. However, unless you do a lot of moving stuff around (like during testing) it is a "once only" event. If you name the new RAID boot volume with same name, might not even matter.
I do a lot of backup and restores during the course of a week, SuperDuper works well, not 200% perfect maybe, but works.
I keep my boot volume, though, free of my home account. That resides on another volume and can last for years. The boot volume gets changed more often. And I think having "home account" (but not /Users) not be on the boot drive makes it easy and avoids some of these problems even.
Re-installing will take a long time (around 17 applications) and could end in disaster as I would have to re-authorise them all, there is a good possibility that the software may be disabled as they are not running on the disk they where originally installed on. The Native Instruments protection scheme is an absolute minefield, recently I updated one of the applications and it took two weeks to get it to run again with many support calls to NI.
If you fancy a laugh goto the NI forums and search for "Service Center" you will not believe what you read some people loose their software for months!
And you are having these problems after using SuperDuper to clone a drive? they should work. One thing to do is make the backup, then use something else to import or migration assistant or merge back to the fresh system.
The first thing I did with Carbon Copy Cloner 4 yrs ago was to clone a system, then clone the clone, and see if everything worked (it did).
I moved my boot disk to a RAID using "Restore" in Disk Utility. If you prefer the command line, use "asr". Either will clone an existing volume. These are built-in tools that are part of OS X.
I actually started by making the new disk a single-disk "degraded RAID pair" using "diskutil enableRAID", cloned the old disk to the new, booted from the new disk and then added the old disk in as a mirror stripe using "diskutil addToRAID".