So, first of all here's my load order, I got rid of calibr universe(book of earache, weapon replacer, thinking there would be some conflict between it and fook, but the problem was exactly the same.)
When installing fook2 I installed EVE with it in the options so here's my load order ;


fallout3.esm
craft.esm
calibr.esm
xcalibr.esm
fook2 - main.esm
fook2 - [[censored]] world and neighbourhood kit.esm
xcalibruniverse.esm
streetlights.esm
darnifieduif3.esp
craft - activation perk.esp
calibrxmerchant.esp
xcalibrmunitions.esp
xcalibrmunitions_fosenhancements.esp
overhead3pcamera.esp
fook2 - main.esp
fook2 - [eve] energy visuals enhanced.esp
xcalibruniverse.esp
xcalibruniverse_repairlists.esp
xcalibruniverse_ammolists.esp
stealthboy recon armor - craft.esp
owned!.esp
fellout-full.esp
merged patch.esp


http://img829.imageshack.us/gal.php?g=screenshot41r.png

Pictured is: What the brotherhood of steel guy looks like while holding the plasma rifle, and then when I ~kill him in the console and take the weapon, it appears absolutely fine on me. I don't know what could cause this, I'm definetely thinking something with EVE due to it being an energy weapon.

After reading some stuff on fook2unity, it says I'm supposed to delete everything except for the Main.esm and main.esp ? :S NOW I'm confused

Simply delete every other FOOK .esp. May just want to reinstall the whole mod, though.

EDIT: last i checked, EVE isn't compatible with FOOK. Or was the FWE? Ugh not too sure.

With FOOK2, you need the hotfixes to upgrade it to 1.1 beta.

The problem in your case is FOOK2 - EVE. This is now in the main FOOK2 plugin, the old version has bad paths to the meshes of the P95 and P94 plasma rifles.

Just don't use FOOK dude. FOOK is just a giant black hole of conflicts. You can find any mod you like in FOOK seperately anyways.