If things were smooth before the parts were replaced and things are rough after the work was done doesn't add up for something simple like the pump.
You can't tell if the shaft is bent unless you remove it from the machine, block it up on the bench and spin it by hand.
You say you did the work last season but did not run it until this season. Are you sure the performance problem is pump related? 30 mph is too slow assuming the pump is set up correct. Even if the thru hull seal is not perfect there should still be descent top end still. If the seal doesn't let water into the hull then it should still work well enough to get you moving. However, double check the wheel mounted in the ride shoe back by the pump and make sure all of the "arms" are on it still. My wife has a 94 gtx that reads slow on the speedo due to a missing arm. That is the sensor for the speedo.
The knocking sound from under the motor you describe sounds like a seperate problem based on your description.
Some grease squishing out when you pump grease in doesn't always mean the seal is bad, most if the time it means you pumped in too much grease. Water leaking in while sitting still, no motor running, or cavitation during the hole shot are indicators a seal should be looked at. However, if you are pulling the drive shaft out you can remove the thru hull bearing, clean and inspect the bearing and seals and decide if they are damaged. Just loosen the hose clamp and it pops right out in two seconds.
As for misalignment? Unless you loosened the motor mounts since you rode last season then everything should be in the same alignment as when it ran good last year.
The factory bearing installation tool you used is the way to go. When you put the thrust washer, thrust bearing and impeller shaft together did you make sure the bearing centered on the shaft before you tightened the impeller down? If the bearing was off center it can be pinched/crushed as the impeller is torqued down, but even that happening doesn't fully explain the performance loss, vibration or knocking.
I would pull the pump and drive shaft out. Inspect the shaft for kicks, make sure that impeller spins smooth without any feeling of binding from inside the pump. Most important, for trouble shooting, start and run the motor with the pump and shaft removed and see if you still get that knocking sound. Just to clarify, is the knocking at all rpm's or just at an idle? If it is all r's then that doesn't sound good. If it is only at an idle then confirm that the rubber bumper plugs are installed on both ends of the drive shaft.