Well the new tie rod end arrived. I removed the old one, and compared the stud length to the new one, and they are the same. I installed the new one, with new hardware, and torqued it to 36 ft-lbs. The hole in the stud is again above the castle nut. So this tells me that I must have yielded the tapered hole in the steering knuckle. The funny thing is, I torqued the new tie rod end on the other side to 36 ft-lbs the first time, and the hole and castle nut line up correctly, but on the under side, there is a gap between the bottom of the steering knuckle and the rubber boot on the tie rod end, as though it needs to be toruqed more to close the gap. That is what I did on the first side, and I guess, screwed up the tapered hole in the knuckle doing it.
Does anyone think I need to replace the whole steering knuckle now? The hole in the stud is approximately 1/8" above the castle nut. I was able to bend the cotter pin head down so it sits into the castle nut recess. I guess this thread would be make more sense with pictures, I'll snap a few when I get home this evening.