How to minimize weirdness after a migration

My MacBook Pro (early 2008) got a recent fix of its NVIDIA card. It also was returned to me with a brand new hard drive (for some reason Apple deemed it a necessary repair). I like starting from a clean slate, but every time I've gone thru the migration process (using Migration Assistant) I have enough slight issues with migrated files that I wonder how stable my system is.
Some examples:
+Tried to launch Final Cut Pro and was asked for the registration again. I would enter the info and the app would just quit. I intend to do a complete re-install of Final Cut Studio when I have time.+
+Various folders and files can't be altered because I "don't have sufficient permissions" to change a filename or whatever.+
+I try to launch some apps but they quit mid-launch.+
Before the computer was shipped back to the depot, I made a complete copy of the hard drive using SuperDuper. After the repaired MBP was back, I used Migration Assistant to move over my original Home folder from the SuperDuper image onto the new drive. I didn't have MA move any applications or other settings thinking I would reinstall apps I truly needed, and not bring over all the ones I'd accumulated but rarely used from the old drive. I still had to manually drag over some Preferences and other related files to get things working. And I still have weird permission issues and random anomalies from time to time.
I have used Disk Utility to repair permissions, but that usually never fixes my ability to read/write to some files.
Ultimately, I'm worried I don't have the cleanest system at this point. How can I best check to be sure permissions are correct and I can start feeling secure about installing more apps (like Final Cut)?
Thanks for reading ALL this!
Message was edited by: chip grabow

chip grabow wrote:
While my original HD and system seemed fine, it was long overdue for a clean system install …
What do you think justifies such a drastic step? Superfluous files are just that, superfluous. They take up a little disk space, but do nothing else. If the OS is somehow using them, then things won't seem fine because they won't be. And if you try a combination of Migration Assistant & manual migration, chances are they won't be either because you have complicated a process that has a much simpler alternative you could use instead.
IMO, the myth that an OS X system needs a periodic 'cleaning' to work properly lingers on as much because it is a self fulfilling prophecy as anything else. No offense to anyone, but the OS is better at maintaining itself than 99% of users are. The more they tinker with it, the more likely they are to cause problems rather than to avoid them.
There are a few very specific problems that require a clean install to correct, but none so subtle they would go unnoticed. And to be effective very specific steps must be taken to make sure it stays clean. But for some reason some users get the idea that these problems will strike them if they don't act preemptively & frequently either ignore the part about keeping things clean or don't know about that to begin with.

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