Ok, so now that I took the steering box off and re-drilled the holes, it turns out that they were lined up perfectly to begin with. BUT, since the TG kit uses 1/2" (SAE), and the truck is Japanese (Metric), I was having some issues. The holes for the mount were perfectly aligned. THe holes in the steering box, however, were smaller than 1/2". I didn't even think to check that since I got the box from TG as well as the mount, and I assumed the 1/2" hardware would fit in the box.
Note to anyone doing steering: check to see if your steering box holes are big enough for your bolts. I assumed the box was fine and blamed my mount.
Now that I drilled out the steering box holes, it lined up perfectly and went in without a hitch. I sure could have saved a few days if I had checked that first. Yes, I'm a moron. The good news is that if I can do it, most people can do it. It's still not a piece of cake on a 1st gen pickup, but I definitely made it harder than it had to be.