Thanks so much for all the great feedback today! This is why my Tweaks keep getting better.

I haven't been able to reply to everything because I've been working on v.4.6 of my new Encumbrance Script.
Strain is now calculated, based on Timescale. I've also made the Strain a bit less harsh.
If you have Timescale set at 1 (same as real time), and when your encumbrance is 50% or less, you will be able to run for 24 minutes before exceeding your Strain Limit.
If you have Timescale set at 4 (like me), this works out to 6 minutes of running (which is still 24 game minutes).
With an encumbrance of 100%, you'll only be able to run for 5 game minutes (1.25 minutes with Timescale set to 4).
With 101% encumbrance, you can now walk for 48 game minutes (12 minutes with Timescale set to 4).
With 110% encumbrance, you can now walk for 12 game minutes (3 minutes with Timescale set to 4).
With 150% encumbrance, you can only walk for 3 game minutes (45 seconds with Timescale set to 4).
Your Strain will now decrease at the rate of -18 Stain/game minute when walking; and -36 Stain/game minute when not moving.
[With Timescale set at 4, it will take 83 seconds when walking and 41 seconds when standing still, to go from 100% Strain to 0%.]
Right now you have your strain code running in a gamemode block, I'm guessing with "getsecondspassed" used to time the lapse between frames. If you added an abbreviated copy of it, just the strain-decreasing-over-time part, to a menumode block in the same script, it would run whenever you're in a menu, and you could still use getsecondspassed. It wouldn't require any changes to your existing gamemode code, so it shouldn't slow anything down.
I didn't mean disable strain while in combat, just prevent strain from decreasing while in combat and in a menu. Otherwise if the player was, say, running away from a radscorpion and got too tired to run, they could cheat and just bring up the Pipboy for a few seconds.
Thanks Imp! And, I understand what you meant now (sorry). I'm not using getsecondspassed in my script, but I was still able to get this mostly working by using a menumode block at the end of my script.
I haven't fully tested this yet, but it works great when you're in your PipBoy menus. Since you're basically standing still when you are in any menu, Strain will never increase . . . so this just decreases your Strain.
But since game time does not actually pass when you're in any menu, I gave a smaller decrease (than what you get when you are resting and not in any menu).
So when you are not in combat, and are viewing a PipBoy menu (I still have to check other menus), your Strain will now decrease at the rate of -12 Strain/game minute.
When you are in combat, your Strain will not decrease at all when you are in a Pipboy menu.
The sleep/wait menu still wouldn't work exactly right (it would count the number of elapsed seconds, realtime, rather than the amount of gametime waited). To fix that, you'd need to check gamehour at the start of entering the wait menu, and again upon exiting, subtract the two, and use that instead of getsecondspassed (after accounting for crossing into a new day if it happens). I don't see that as being as crucial though.
I put together a HUD counter template (an .esp and the necessary xml files) that works with or without DUI installed, and uploaded it to Nexus along with instructions on how to modify it to incorporate it into other mods, so if you want to take a crack at adding a strain meter (and maybe encumberance too, though DUI's already got that) it should help.
http://www.fallout3nexus.com/downloads/file.php?id=12977
For now, I'm not going to reduce Strain when waiting or sleeping, as I don't really see the need. Strain decreases pretty fast when you are not moving, so I view this as time needed to fully wake up.
I'll take a look at your DarN HUD file, but all that menu stuff may still be more than I can grasp.