Having recently fubar'd my own game i can associate lol.
1st steped probably missed was rolling back SH3Commander before adding or subtracting any mods
but since you have your stock version working you are well on your way to recovery.
The steps i took were to get the game running, bring it up to 1.4, installed gwx, installed the 1.03 mod. Installed jsgme 1.7 installed sh3 commander and the files into its config folder for gwx then i used jsgme to install the mods i wanted then refired up the game and all works well.
Hope that helps
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