1. I'm not sure of your problem, but I get the impression you are trying to run a server from the COD4 "main" folder (hence why you weren't looking in your mod folder). Mods WILL NOT RUN in the "main" folder. IW have restricted all mods to only work in mod folders (i.e fs_game folders). So, you cannot mod a ranked game in any way. The game will simply ignore any mod files you put in the "main" folder, as if they weren't even there; they will be invisible to a ranked game.
If I have misunderstood you on this, then I apologise.
3. You can stop GSC files downloading in 2 ways:
1. put them in a raw folder on your server. They wont download to anyone as raw folders don't download to clients;
2. Put them in an IWD file, with "_svr_" in the IWD file name. Just like in COD 1 1.5 and COD UO. IWDs with "_svr_" in their name don't download to clients.
4. You cannot stop Deep Impact with any kind of physics trace (bullteTrace or otherwise) to return on if found because it is hard coded. Where would you put the code? What file? There isn't one!
The only way of restricting perks from a player's saved class data is by intercepting them on the class loadout ( maps\mp\gametypes\_class::giveloadout() ). There is a function there to set any perks on the player. Simply intercept Deep Impact at that function and unsetPerk() on the player if Deep Impact is found. You wont be able to take it out of their saved class data, but it will stop them being able to use Deep Impact during a game.