"Trawling through" or "trolling through"

Trawl and troll are both fishing methods. Trolling is when you drag a line behind a slowly moving boat. Trawling is trolling with a net.

Trawling is more likely to be associated with commercial fishing and a large catch, so I would guess this would equally imply harder work than trolling, although the terms refer more to the idea of catching something than they do to how difficult that endeavor is, so either term would work in your context.

Trolling, on the other hand, can also mean baiting someone online, so it might cause confusion or have a negative connotation.

That said, I think you would be understood best if you said something like "I had to trawl each script to find the called files."

I honestly can't remember ever hearing the term "trawl/troll though". Generally, I hear people say/write "go(ing) though each script".

Edit: As Kristina pointed out in a comment to this answer, "to comb through" is often used to specify checking something carefully. my guess is this stems from "To go over with a fine tooth comb".