OK, as per the documentation in CMS, your game folder has to be "Silent Hunter Wolves of the Pacific", which is what the default Ubisoft install folder name is (or edit the batch files to use something else). Try changing the name of your "Wolves of the Pacific" folder to that. Have the CMS folder in the "C:Games/steamapps/common/" folder. Steam may not like this at all though, and you might have to go through the Steam Library app to change the folder name, and then it also might not like you putting the CMS folder in there. It will depend upon your computer and it's set-up.
One ~really~ big thing - that Steam folder is Write Protected, so you can copy folders and files into it (usually), but a batch file, which is what CMS uses, can't. It won't even throw an error message. So you have to right-click on that "common" folder, and then on the "General" tab, tick that "Read-only..." box so that it clears, then left-click on the "Apply" button. It will then ask you if you want to apply it to all the sub-folders and files, which you do... It will then run "Applying attributes to:" for a while. It was like three minutes on my computer. If you have several games in the folder, it will take longer. I've got SH3, 4 & 5 folders, and that's all.
Once you have the SH4 folder renamed to "Silent Hunter Wolves of the Pacific", and the "common" folder Write-enabled, then you can run CMS and create an "SH4 Pristine" (choice #2) from your files - But your game has to be a "fresh" install. No mods applied yet. After that, ~then~ you can create the other install folders for mods. Now for a caveat: This is on ~my~ computer. I have no idea how this will work on yours. I have an older Intel Duo-Core Quad Core computer with 8gig of ram, running Windows 7 SP1 64-bit... ymmv
One last step(s): Add the modded game folder to your Steam Menu... here again, I'm not sure if this will work with your Steam install, but what I did first was rename the SH4.exe file in my newly created "SH4TMO" folder. I changed it to SH4TMO.exe to match my folder. Then I was started the Steam app on my computer - NOT online, but on my computer. Next, log-in to your account. You should get the "normal" Steam app (after it does its normal "updates"), with a small-sized dark grey text menu up top (Steam, View, Friends, Games, Help) that is somewhat difficult to see on my computer. The bigger menu has the Left / Right arrow keys, then "Store, Library, Community, then your user name. You want to click on that small Games menu choice up top. On that little menu, click on "Add a non-Steam game to my Library". Click on the "Browse" button, then drill through the FileIOdialog box "Add a Game", to the correct folder and click to select the SH4TMO.exe (in my particular case), then on the "Open" button (or just double-click the SH4TMO.exe). That will take you back to the Steam "Add a Game" dialog box (black), where you then click on the "Add Selected Programs" button. Viola! There it is on the menu choice, and lo and behold, it actually ran on my computer...
I was going to post a few screen grabs, but Imgur is down right now, so I can't upload any files, so maybe later. If you try this, let us know how it goes for you.
Edit: I forgot to mention that you should either change the name of your original Steam folder back to the way you had it, or make a copy of it and change the copy's name back, so that Steam can find its install. Just remember that CMS needs to "see" that "Silent Hunter Wolves of the Pacific folder for it to run, unless you edit the batch files (*.bat) instead...