Small texture or sound mods that don’t give you any particular advantage are fine, like “Cosmod”, I think some HUD modifications are alright, like getting rid of those two lines around the outside of the crosshairs that show up on some builds. I don’t see anything wrong with SweetFX, just makes things look a little brighter and sharper.
Some tools are allowed: http://wiki.sourceruns.org/wiki/General_Run_Categories_and_Rules
It doesn’t list SPT, but if you’re running scripted, I don’t see why SPT and it’s autojump would be a problem, if not, use AHK.
Cinematic mod, but that’d be a whole new category because the whole thing is so different, you could probably find routes that’d be faster than in the unmodded game with the Cinematic mod.
You could probably replace weapon models and stuff but people would hate you if you did.
People who speedrun don’t really modify their game, in fact it’s rare, the only “major” mods you’d see are names of chapters, bump-mapped versions of the same textures or the credits, and on some occasions, a different HUD, but people don’t really mod their speed games to make the more aesthetically pleasing.