Strange, but PESE is that GoG says it's selling, and the thing that made the Special Edition 'special' was the inclusion of the mods - so they should be on your GoG version somewhere. On first release, the mods came on a second 'bonus' cd with the mods, a few other things like destkop wallpaper and the editors. Possibly apart from the wallpapers, I think you can now get the editors and the mods on the PEDG website...
http://pedg.chollie.co.uk/
...with some newer mods (or reworks of the original mods) instead being available on the PEDG forums...
https://www.tapatalk.com/groups/pedg...138b3ab363aebb
I dunno if GoG bundled the original mods or the later ones but they and the editors (landscape, object and scenario) should all be there somewhere. On the PESE 'bonus' CD, IIRC each mod was a separate self-installing zip file. If you look at the folder structure of your installation, there should be some clue, maybe a 'bonus' folder or somesuch. IIRC the panzer history was part of the paper manual.