How do I fix the ridiculous collision box around the doomstones to fit just around it instead of reaching miles into the sky?

It's not, if you remember how the doomstones operate they shoot a beam of light up into the sky. The nif has NiNodes up there so the bounds actually reach up that high.

Collision is different it's a rough invisible mesh that gives collision which is independent of the bounds of the nif. From what I can see the obelisk node is the only one with collision, and yes you can jump over the top easy enough so there's no problem with it.

Only the Thief, Tower and Mage stones have that hugh bounding box. What's the easiest way to make a version of those stones that will still work like the origionals but have a smaller bounding box?

I tried copying and renaming then using the model from the loadscreen magestone but it wasn't activateable even though it still had the script.

The loadscreen uses a different nif with none of the extra data that the in game nifs have, it's that extra data (all the funky stuff) that makes the bounding box huge. I suspect what your comparing here is loadscreen to activator nifs and there is a big difference in the nifs.