The Ames studs came in while I was gone. It's a good thing I'm not a surgeon. I screwed these bad boys in backwards (thick threads into the water pump is not the right way, doh!) and had to stop myself before I completely ruined my new water pump. The fine threads go into the water pump, which is counter intuitive because they are too long. The coarse threads stick out and that's where the nuts bolt on to hold the fan and belt pulley.
Lesson here is that if it takes a ton of pressure and acts like it doesn't want to go, even though it's brand new, you are probably doing something wrong. Stop, think, don't force it. I was lucky and was able to back the studs out and put them in the right way. I'll have to keep my eye on these studs when I get the car running.
Once I got them going the right way, I used two nuts tightened against each other so I could get the studs all the way in.