Update
I guess i got lucky. The pump is now back in the boat after a wrestling match from hell with the impelller. We ended up having to cut it off but its now all back together and much tighter. There was not rocks or any damage in the bowl or impeller beyond a few dings but I got the master rebuild kit so I replaced it anyway. It had however been hitting the wear ring so thats where the chirping had been coming from. The bowl bearings may have had a little wear being as they are more like bushings than bearings its hard to tell and the old thrust bearing seemed ok.
The u bolts on the universal joint were also a little loose so im sure thats where most of the vibration was coming from so I dont want to say I wasted time and money rebuilding the pump but Its all fresh and now I dont have to worry about the condition of it anymore.