Your English is probably better than mine. I've learned entirely too much slang over the years, and how to mangle the King's English to a "T", to the point that no translator program can translate what I write. Just ask s7rikeback!
Anyway, it does sound like you are cross-contaminated. If you have a Steam version of the game, you do have to run the game first to set the license properly. Changing the video settings only before applying the mod, might cause an issue... [Thinking Out Loud] The mod will overwrite the game folder's Main.cfg... that may well be a problem there, since the game uses what it finds, and will not overwrite the Save folder's copy of Main.cfg...[/TOL] I would say then that you should delete the SH4 Save folder, back off the mod, then re-apply the mod and run the game, re-setting your video to the proper resolution, and all of the other Options on the menu. Quit the game so all of that takes, and try playing it again. If you notice any further issues, you might be stuck with having to do a clean re-install of the game, along with emptying the Save folder again.