Overall, Trigun Stampede adheres closely to the manga. Some minor details might differ for the sake of the adaptation's flow and visual presentation, but the core remains the same.
It's quite accurate. The anime version of Trigun Stampede mostly adheres to the manga, with just a few minor differences that don't significantly impact the main plot or character development.
I think it does to a large extent. There might be some minor tweaks here and there, but the core plot and characters are pretty much in line with the manga.
Trigun Stampede takes some liberties compared to the manga. It changes certain story elements and character traits to offer a fresh perspective, but this might not please all manga purists.
I'm not sure if there is a specific 'naruto is trigon fanfiction'. But if it exists, it might be a very strange and creative crossover. Maybe in this fanfiction, the world of Naruto somehow intersects with the concept of trigon, perhaps Trigon's powers are introduced into the Naruto universe and change the way ninjas fight or interact.