I know that there were some pumps out there that used screws to hold the wear ring, but always thought they were some of the older 2-stroke ones. I was always under the impression that the 4-tec pumps do not use screws... I haven't worked on enough of these to be any expert though.
I do agree that the new pump housing and bearings should solve your problem. Just be careful assembling everything so that it is true and strait. Have never assembled the bearings into a new housing before but I know it is easy to get things out of alignment if you are not careful. Also, make sure the impeller is in good shape and clean up any knicks with a file or dremmel if they are not bad.
If you are still worried about the drive shaft it should not be that hard to remove and check at this point. Just loosen the bellows clamp, and the circ-clip from under the SS ring and it should slide right out. Then you can check to make sure it is not warped for piece of mind and clean it up if it needs it.
As for what causes the pumps to warp, I am not exactly sure. I would thing that over torquing the bolts is a logical reason as it might not allow everything to expand properly as it heats up. Also, if it was cavitating real bad and someone revved the crap out of it, the pump could heat up. I have seen pictures of wear rings that have been melted like this.
Anyway, I think you are good to go once the new parts arrive. Also, I commend you taking on such a project yourself being kind of new to these boats. Good luck and let us know how it all turns out!