[masraum]

I'm voting, if you can, go cat 6. Make sure that you purchase everything together and matching (stranded/unstranded, only cat6, etc...) Anything that you have laying around that is not cat 6, throw out or lock up somewhere so you don't end up with a mix and match setup. It probably wouldn't hurt to have a couple of cable testers. If you're going to do this, do it right with lots of labeling and organization.

The one "issue" that I could see coming up is that you're changing hardware, moving stuff around, and recabling. If you have a problem, which of those things caused it. If you do it all at once, it will make troubleshooting the inevitable issues more complex. It would be nice if you could make the changes separately. IE, change, move the hardware using the same cables. Make sure everything works and then change out the cables (or the other way around, whichever is easiest).