The key to getting JSGME to work with CFS3 is that the MODS folder needs to be outside of CFS3.
http://www.softpedia.com/get/Others/Miscellaneous/Generic-Mod-Enabler.shtml
I have a single copy of the JSGME program installed, and then created multiple desktop shortcuts for each of my 16 CFS3 install locations.
Open the shortcut and set the Target location to S:\JSGME\JSGME.exe (or wherever you have JSGME.exe located), and the Start In: to "C:\Program Files\Microsoft Games" (or wherever you have the MODS folder located for one of your CFS3 installs).
For the normal location C:\Program Files\Microsoft Games the MODS folder is at C:\Program Files\MODS.
JSGME will create C:\Program Files\JSGME.ini the first time you run the shortcut.
Its contents will look something like this:
[MODS FOLDER]
Name=MODS
[JSGME DETAILS]
FullPath=S:\JSGME\JSGME.exe
[FORM SIZE]
Main Height=529
Main Left=396
Main Top=693
Main Width=676
Main WindowState=0
Inside the MODS folder you will create folders that contain the modified files that you want to add or exchange with the originals.
At the top level (1) the folder needs to have a descriptive name for the individual mod. (For example 25 Feb 17 Shaders - Bob, Weather Mod - PTO, etc.)
At the next level (2) is a folder named the same as your specific CFS3 install. (Combat Flight Simulator 3, CFS3 PTO Rising Sun, DPC CFS3 Korea, etc)
The next levels (3+) are all the various files and folders that make up the mod itself. These need to be structured that same way they are in the game directories.
As you add and remove mods it will write a file at C:\Program Files\MODS\JSGME.ini (I know, using the same name again is confusing, but that's what the programmer chose to do)
Its contents will look something like this:
[DEPENDANCIES]
Feb 2016 Gunsight Shaders - PTO="25 Feb 17 Shaders - PTO"
[MODS]
New Composite Budgets - PTO - No Stutters=1
Weather Mod - BoB=2
Weather Mod - PTO=3
Feb 2016 Gunsight Shaders - PTO=4
25 Feb 17 Shaders - Bob=5
25 Feb 17 Shaders - PTO=6
Don't mess with the !BACKUP or !INSTLOGS folders inside MODS or you will destroy the ability to restore the original state of your game.
*** Once you've created the level(1) and level (2) folders in the JSGME MODS folder, you can directly unpack everything in the the zip file for AnKor's Shader package there to populate level (3+). ***