Ok, sounds like a factory reset is in order.
Some tips to keep your performance up
When you hold c and boot off the 10.6 disk and use Disk Utility to erase the drive, use the Security Option > Zero option (it should be GUID OS X Extended Journaled formatted)
This will map off any bad sectors you may have, it takes a bit to complete, but worth it later as your reads will be as fast as they can be. (no slowdowns trying to read bad sectors)
Next when you reinstall OS X, setup with your same user name, this way certain files in iTunes and such work, then Software Update fully, then install all your third party programs and then last your files from backup, in that order.
Do not restore from TM drive, so that means you need to have your user files on a external storage drive beforehand.
Also keep the boot drive ideally less than 50% filled, but never more that 75% filled.
Once your data goes past the 50% mark you start losing drive performance.
Another option is to clone your present 10.6 drive to a blank extenral drive with the free Carbon Copy Cloner, that way you have a 'hold option key' bootable copy of everything.
Good luck 🙂