Q: Need directions for Mavericks clean install (w/o Migration Assistant)

I'm looking for a how-to article or some guidance on doing a Mavericks clean install. Since upgrading an Early-'08 Mac Pro to Mavericks, I've experienced slowness, unscheduled wake-ups and a non-working keyboard on wake-up. Sometimes, I have to do multiple reboots to get back to where the keyboard is recognized.

I have a new HD and am planning to reformat and then do a clean install to Mavericks. Not sure if it makes sense, but I was going to manually move and reinstall programs and files as an alternative to possibly re-importing bad settings, problematic software settings and that sort of thing by using the Migration Assistant.

Doing a reinstall of Mavericks onto a new HD and then using Migration Assistant to transfer everything didn't work as planned. I'm still experiencing the same problems, which may be hardware-based. A clean install will remove most doubt. 

Is there a tech article on how best to do this? Specifically, moving things like Mail folders, iTunes and that sort of stuff.

Everything I've found says to use Migration Assistant and automatically drag everything across. Reinstalling programs and moving data files will be a PITA but seems like a logical next step to eliminate software based problems and generally eliminating a lot of old files and settings that may slow things down or interfere. 

Thanks,

Rich H. in Seattle