I did agree for each mod to overwrite the files when doing it manually, taking care to install each mod on the correct order as instructed. JSGME says that some files have already been altered by X mod, however installing in the correct order, particularly with the patch files, shouldn't produce this issue?
The errors I get include:
File not found: data/menu/data/black80.tga
There is a new (not implemented) page: <PageChooseLoadSave? !
File not found: data/menu/skins/american/gui/intelligenceunits/paper.dds
File not found: data/menu/skins/american/gui/layout/Dials_us_metric.tga
File not found: data/menu/skins/american/data/recognitionmanual.tga
File not found: data/menu/skins/american/gui/clock.tga
File not found: data/menu/gui/tdc/tdc_metric.tga
File not found: data/menu/gui/strategicred.dds
File not found: data/menu/gui/strategicblue.dds
File not found: data/menu/skins/american/gui/layout/navigationtools.tga
File not found: data/menu/data/awardsitems_4.dds
File not found: data/menu/data/awardsitems_3.dds
File not found: data/menu/skins/american/gui/careertransfer/transferboard.dds
File not found: data/menu/skins/american/gui/careerstart/careerwheretostart.tga
There is a new (not implemented) page: <Page PlayerRank> !
File not found: data/menu/skins/american/gui/player rank/left papers.dds
File not found: data/menu/skins/american/gui/player rank/tabs and paper.dds
There is a new (not implemented) page: <Page IntelligenceUnits> !
There are more but I think this spells out the general gist - the installation of these mods, even in the correct order, are disposing of various essential files?
I tried to verify the files using Steam, but this seems to just remove all the mods that have been installed, returning it to the base game stating "10783 files failed to validate and will be reacquired." which tells me the mod install deletes essential files! Frustrating!