What I suspect is going on with that stage (and a couple of other similar ones) to make the effects pop so well is that they pass some variables to the shaders that vary their intensity. I really wish the shaders were runtime-compiled, so we could see what's going on with them and rewrite them (esp since shader programming is another one of my hobbies)... Anyway, you should be able to swap it between stages just by replacing the Setup_Params.lua (i.e., just like swapping the lighting).
As for the perspective distortion, that's all user-editable in SFxT via plaintext files, which is awesome, but it's buried in the executable in SF4. I had hoped they would update the SF4 engine to match at some point, but it never happened. You could probably do some twiddling in Cheat Engine, but that's made more difficult by the fact that SF4 intentionally crashes if you try to attach a debugger. I think some people have gotten around that somehow, though.
Just delete the modded files and have steam verify the local cache.
If none of your changes are showing up, the files are probably being overridden somewhere. Try putting your modded files into the [latest patch]/battle/chara/*** folder (you may have to create that structure if it doesn't already exist). All of the tutorials are linked on the wikis (sf4mods.pbworks.com and aemods.pbworks.com).
That darkening on the EMO is caused by baked-in ambient occlusion maps. Sloth86 made some tools for dealing with them and I wrote a tutorial on how to use them. Hit the tutorials page on the wikis to learn more.