Webster

seams like you got the rest sorted out already so i'll just address this part

I found this happened to me all the time when I first tried the eye patch.

this mod was needed for a select few older video cards and I think it was just something to do with the drivers for them so while only a limited few people ever needed it to begin with, you no longer need this mod at all for the game.

the problem with this mod is it causes irreversible game corruption you cant fix so the only remedy is to uninstall the game, manually go into your computer files and delete the sh4 folder found in your "C"drive/programs files, then delete the sh4 folder in your documents folder and do a fresh new reinstall off the game. then the eyes will be normal again.

if you have a clean unmodded backup copy of the sh4 "data" folder, something everyone should do for insurance against corrupted game files, then you don't have to reinstall the game, you just need to delete the "data" folder in your programs files found inside the "ubisoft/sh4" folder and copy and paste a fresh new version in its place.

as for your mod list i'll see what I can add to what has already been mentioned above

#1 Real Environment mod install
3000 Yard Bearing Tool (1920x)
3000 Yard-Meter Bearing Tools (1280x960)
Bigger Better Protractors
Extra Allied naval bases for SH4 + UBM + TMO v1.7 (v1.0) pretty sure this one is only supposed to be used with TMO v1.7 or not at all
Eye Patch for Stock never use this mod unless you already have eyes missing, it causes them to disappear and corrupts the game files
Game Fixes Only Mod v1.1
GFO Patch for Real Env
GFO Patch for RSRDC v401
GFO Snorkel Name Change
Magnified Hud Dials for v1.5_Large
MaxOptics IV for GFO 1.1 im pretty sure you can only use one version of maxoptics at a time, not both
MaxOptics3 for SCAF 1.5 im pretty sure you can only use one version of maxoptics at a time, not both
Metric Nomographs
Nav Map Make-Over v2.1
New Orders Bar Menu
NMMO v2.1 Patch 1 no AB
Remove grain effect
RSRDC_SH15_V400 you can only use one version at a time, not all 3 versions at the same time
RSRDC_SH15_V401 you can only use one version at a time, not all 3 versions at the same time
RSRDC_SH15_V550 you can only use one version at a time, not all 3 versions at the same time
RSRDC_V4XX_Patch1 only use one version at a time, not both at the same time
RSRDC_V5xx_Patch1 only use one version at a time, not both at the same time
SCAF for SH 1.5
Sobers compass mod_version color
TDW_Ship_Plane_Fire_Damage_v1_3_SH4
US Torpedo Test Mission
Webster's Eliminate Floating Plankton
Webster's Improved US Torpedo v2
Webster's New sonar view for v1.5
Webster's No Crew Fatigue
Webster's Ship Manuvering Fix
Webster's Upgraded Deck Gun v1

the key with GFO is its designed to be used "first" to patch or fix the game issues and make a few "minor" eye candy fixes as well

all mods should be added to the game after GFO except where specified such as my patches for mods used with GFO

using mods on top of GFO can "sometimes" undo changes made by GFO and revert some aspects of the game back to stock but they shouldn't cause any issues with the game otherwise.

think of GFO as the last patch for the game that ubisoft never made for it, and just like the stock game you can use "just about" any mod you want to use with it and at the worst you just undo some, most, or in the case of the large super mods like FOTRS, TMO,RFB, they will undo all the fixes made by GFO so its pretty pointless to use those mods on top of GFO but you can, that's pretty much the way I designed it, so GFO is infinitely moddable and compatible with "almost" any mods