You folder structure looks fine, though I'm not sure about using removable drives... but first thing for you, is to make certain that you have the correct folder that has Silent Hunter 4 version 1.5 in it, which is the Uboat Missions copy. There are a couple of ways to figure it out. One way is to look in the game's "Data" folder, and if you see a folder named "UPCDataGE", that is the correct v1.5 - that folder is not in the v1.3 game. Another way is to right-click on the SH4.exe file in the game folder, choose "Properties" from that menu, then click on the "Details" tab header, and right in the middle of that page should be "Product version: 1,5,0,0".
OK, after I do the initial install (for you, you have to run the game once to get the Steam license updated), I go to the inside of the game folder, which in this case, for my example, is SH4 Pristine (10 bonus points if you know the utility I used to get this install). I then press <Ctrl><A> for a "Select All" short cut, which gets me this:
(pretend you don't see all the files associated with JSGME, LAA & MultiSH4)
I then right-click in the blue area of selected files, which on my computer brings up a context menu with a 7zip choice on it for "Add to archive". Else you can start your favorite archive program from the Start menu. Here is the dialog from 7zip:
I press the "OK" button, and it adds the folder contents to a zip file, using the folder name, which you could change if you wanted. When it's finished, you should have an archive file:
Copy that archive file and paste into any of the game folders you have in your "Games" folder. Here's a picture of my folder, which includes more than Silent Hunter games:
The "Validator" folder is a utility from TDW that I use for modding, the "Terrain" folder is a GWX utility for modding terrain height, and the "SH4CorruptionManagmentSystem" is the utility from Rockin Robbins that I now use for most of this type of work, but I will still usually change my folder names to suit me. I am not sure if it would function as intended with a Steam install. We'll have to try to find that out...
Notice that I have 3 FotRSU folders right now. One previous, one current, and one for modding. Anyway, after I have the folders created that I want, I copy my "SH4 Pristine.7z" file into them, and extract the archive. It is much faster moving the archive than it is copying it, or copying the game files, but do it however you like. After I've got the game in other folders...
I then bring in a JSGME, MultiSH4 & Large Address Aware. Right-click on your SH4.exe file, and select "Properties" from the context menu. You want to make certain that it is not write protected on the "General" tab. If there is a checkmark in the tick box, un-tick it and press "OK". You have to do this in each folder with a copy of the game that you've created. I usually run MultiSH4 next to create a new Save folder for the game copy. All of the copies that you make should have the MultiSH4 run on them, to get yourself a new Save folder. My "My Documents" looks like this:
CMN
F80
F81
FOTRSU
GFO
GWX
NYG
LSH
OPM
SH3
SH4
SH5
TMO
V14
V15
Yes, there are other things besides SH4 in there... I do have a Steam folder also, with several SH3 installs modded. My SH5 folder is actually a TWoS install... But I digress - and yes, I need a bigger hard drive
I then run LAA, because the MultiSH4 will sometimes fail after you've altered the SH4.exe with MultiSH4. It also will fail if the file is write-protected. After that, run JSGME and bring your mods in.With a Steam version, I would leave the original Steam install where it is. You can run that to play Stock.
One big difference between my disk-based SH4 install and my Steam SH3 and SH5 installs, is that if I goof anything up bad enough with the Steam install(s), I usually have to delete the copies, uninstall the Steam game - which actually only deactivates its license, then delete the install folder on my hard drive, and re-download the game again. That has only happened to me once in several years of SH3 play (tapping on wood for "luck")...