How do I disable the countdown timer for the warthog run in d40? Does anyone have any useful information for how to do this?

Extract the scripts from D40 using Refinery's Data Extraction.

in the Scripts.hsc is the script timer_begin

Delete everything except for this;

(script dormant timer_begin    
        (wake trench_jeep_test)
)

That'll disable the timer from starting, and you should still be able to proceed through the tunnel until you get to the end triggering the cinematic. But a lot of scripts for those encounters pause or wake the hud timer, not sure what's gonna happen. Not gonna compile the map and play through all of D40 to find out for you either. Do post back if you have trouble though, I'll be happy to try to help figure it out.

Um... what do I use to edit the script? Mozzarilla? A basic txt program? And then how do I make sure it's properly compiled into the map? I've never touched scripts before.

Extract the scripts with Refinery, edit them with Notepad or preferably Notepad++

Save them as filename.hsc in the same directory as the scenario.

compile them in Sapien with Ctrl+Shift+C

Sapien? Sapien doesn't like me very much. Every time I use Sapien for pretty much anything, something always goes horribly wrong. I hesitate to use Sapien, especially for scripts, as the earliest trouble I had with a mod was when I made my 1.0 version of a10 last year, and I had to redo the entire level from scratch because a script got screwed up.

What happened was that the blast doors, which are supposed to close after the player finishes the circular staircase and passes through another hall with two grunts and an Elite behind an energy shield before reaching the lifepod hall with the three Grunts (where the light show occurs), ended up being triggered to close before the player reached that point. I know this because Cortana's dialogue regarding the blast doors appeared just after reaching the top of the staircase.

I had to redo the whole level from scratch, and I've only ever touched Sapien out of curiosity since then. To this day, I still cannot figure out what exactly I did to cause that scripted event to trigger early, but I've been wary of using Sapien for anything since then.

Mozzarilla has a "compile tag" function, doesn't it? Would that perform a similar function, or can hsc scripts only be compiled using Sapien?

To this day, the only way we can compile scripts is with sapien. Nothing else can.