I found a chromolly road stem in the bargain bin at a bike shop. It's for a 1 inch threaded fork. The bolt for tightenning it is way down inside a hole. I think you stick a long allen wrench in there to tighten it in the fork. I think this design makes it light because you don't need a long bolt.

That leaves a 2 inch deep hole in the top of the stem. I'm guessing this should be plugged with something to keep rain from puddling in it. What is the standard solution for this?

Or should I just put a cork in it? (I'm just too good of a straitman)

actually, little laboratory test tube corks work great fi you don't want to hunt down and pay for the appropriate cap. I'd just rub the sides of a test tube cork down with beeswax and shove it in there. When you need to change something, you have a handy tool in your liquor cabinet for that!