Question about Backing Up apps and using Migration tool

Since installing Leopard on my G5 PPC, I have been having a strange problem with the sleep, screen saver. Anytime the system goes into screensaver or sleep, it will not come back and will be frozen. Needless to say I was told by the Mac Genius guys that I need to do a clean install.
So my real question now is about backing up all my apps and then using the migration tool to bring them back into the new install. I was going to attempt to use Carbon Copy Cloner on a second internal drive (Time Machine has never worked for me on my Lacie 500gb.) Once I have a full bootable copy, I will do a clean install (erase and install option) on my original drive, then I guess I am going to use the migration tool.
So my questions are:
1) Does this strategy seem like it will work?
2) Is the migration tool straightforward? IE - Can I pick and choose what to put back on the new install?
3) Any pitfalls that I should be aware of?
I have already backed up my docs and data to the external, but I have so many programs with plugins installed that getting my apps back the way they are is essential to me.
Thanks.

Remember Time Machine is designed to do constant, incremental backups of your HDD. If you delete something from the internal HDD of the Mac it will no longer be backed up to the external HDD and will eventually be deleted from the backup archive as time passes and TM keeps doing its backups.
What will probably be a better solution is to simply drag-n-drop the entire iTunes folder to an external HDD for backup and use that as the main iTunes library. The drawback to this is that to play the music you'll need to have the external HDD connected. Unless your plan is not to delete all the music from your MBP, just some of it.

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