You should be fine with the version you have cebergquist, other than to double-check what you mean by "latest version"? Are you referring to maybe that you have a disk version, and you've applied the v1.4 Patch from Ubisoft to it? Or, are you referring to that you either bought the Uboat Missions Add-On and applied that, or you have the full "Gold Edition - Silent Hunter: Wolves of the Pacific" version? Post back with that info.
Now, the folder structure... "D:" is for drive, whatever yours is, whether C: or D: or E: or whatever. It sounds like you have a "Downloads" folder there, or maybe in your User / My Documents folder, but either way, whether "D:\Downloads..." or "D:\Users \Your Name\ Downloads...", you should have a "Silent Hunter 4" folder of some form, since some files will reside outside the other folders, so you would really want "D:\Downloads \Silent Hunter\MODS...", and your mods in that MODS folder. The game's "Data" folder is on the same level as the "MODS" folder, as well as "Resources" and / or "Support" and the like. Notice that ETR3(SS) has the same basic "path" below his "... steamapps / common" path? Post back with the path to where your mods are, please.
As Aktungbby says: "Welcome to SubSim!"