Clean Install and Time Machine Restore Questions

First, I want to ask how much of your hard drive is filled? When is the last time you cleaned out your cache from your web browsing? When is the last time you rebooted your machine?

A near full hard drive can certainly slow down any machine. Consider looking at that before you do a fresh install. In my experience a fresh install with a migration of files from a time machine backup did not require all software to be "re-installed" and then of course re-registered. I cannot recall what software was botched up though. Even if you have to do that, you have all of your install discs so you should be ok. As far as e-mail, how is e-mail stored for you? On a server or locally? Locally, you just need to make certain that folder is part of your time machine backup or manually back it up. Better safe than sorry. Finally, you may notice a bump in speed but if you're taking an 80% full hard drive and adding it back onto your machine after a fresh OS install, you're not really dealing with the actual problem (if that is indeed part of your problem).