Also know that you need to apply a config file patch to SH3 Commander to work in combination with GWX3. May be what you downloaded already has that incorporated. Better be sure and verify if it is included. I am not fully up to speed with the current releases of mods. It used to be a zip file containing files and folders that need to be extracted to the SH3 Commander install folder, NOT the GWX3 install itself. It may also exist as a self extracting executable.
It probably does not make a difference for your manual targeting issues, but without that it will cause problems in your campaign in the long run.
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