I've tried in the past to change the position of the energy bar to be vertical. I've had limited success in that a vertical energy bar does appear in the desired position, but no matter what I do I can't seem to get rid of the stock one, which is in its usual place. Is this a hard-coded thing? I tried everything I coudl think of (which, admittedly, wasn't much). I was sure to edit both the 1playerhud file as well as the second 1playerhud file found within the PC folder.
What does the hudtransforms.hud file do?

yes it is hardcoded, you cant edit the shipped hud, you can only add new stuff to it
(i hope i remembered this correctly, repsharpshooter found that out when he made the 1.2 hud)