Clean install of OS Lion after Target disk mode transfer

Not sure if this is the right community to ask this in but if you could help me I'd appreciate it.

I have a iMac 5 1, duo core 2 duo with 3 1/2 gigs of RAM. I recently did a targe disk mode transfer of files and folders from my mac book laptop. Mostly because I wanted the software (Creative suite, capture one, etc ...) My computer has slowed down noticeably since then. But what worries me more is the possibility that as a result of the target disk mode I copied a lot of "junk", like .plists scripts that either don't work or don't need to be running, or junk on my local storage. I tried my best to clean off a lot of this stuff, and even did a repair disk permisions (there were a lot of permissions that needed to be repaired quite naturally). Well anyway I bought the 10.7.4 Lion upgrade from the app store. I'm wondering, would it benefit me to do a "clean" install either by partitioning my disk or using a bootable USB. Or an erase and install. Will doing either erase my software and will doing it clean out my HD at all.

Thanks.