Water pumps go out. Put it back together the same order you take it apart and you will be fine. Also take a good look at the balancer. When the rubber goes bad it can slip and screw up your timing marks. You could be running mystery timing.....
Caution on the Spec 3 clutch. The T-5 is not the strongest transmission. I think you would be better off with a clutch that is a little more forgiving. The Spec 3 will hold a ton of power, the T-5 will not. Better to have a clutch that will slip just a little and not shock the trans so hard. Your T-5 just became the weak link.
Sorry, I saw that the H20 pump was not out. Just a hose leaking.