You will want to consult
Moving a Steam Installation and Games on the Steam Knowledgebase site. SH3 and JSGME both are "old" Windows XP programs. With the introduction of Vista, Windows introduced User Access Control (UAC) and other 'technologies', which restricts edits in the Program Files folders, and all "system" folders. Ostensibly, this is to protect the user and MS's OS from unauthorized intruders, such as worms and viruses, etc. However, JSGME is not "authorized" by Windows (being an "old" program) to make the cfg file and other changes, and therefore what Windows deems to be "system" files are rolled back, resulting in a mish-mash of Stock and GWX.
Make yourself a "Games" folder, or similar, and put your Steam games in there, or if you have a viable second hard drive, make a new Steam Library folder there, and install SH3 in there.
Even the disk version of the game does the same "default" install location of Program Files (x86), resulting in the same mess. Change the install path to a folder you make yourself, and put the game there. Another aspect to be aware of is the "help" that the 'modern' Windows gives the user with their video stream. Newer programs communicate with Windows, whereas SH3 doesn't have a clue what is going on in the background, and doesn't "understand" some of the techniques used by Windows to make things "pretty". You probably also have to use the SH3.exe "Properties" settings to make things "compatible" with Windows. This is a Windows 10 example of an SH4.exe screen on one of my computers:
The little "window" on top is from pressing the "Change high DPI settings" button. On one of our laptops, I have to use all the settings there. On most, just that "High DPI scaling override" section. With SH3, you do have to use the "Compatibility Mode" box, and on my machines, I set SH3 to "Windows XP", other folks use different settings. Experimentation is the name of the game. You have to get stock (the Steam version is v1.4b already) running correctly first, then do the mods and try more experiments, if necessary.
