Gentlemen,
I'm thinking we want to ensure your clean Il-2 game is working. Start your clean game and do everything you want to do once you have VP Mod installed. Example: open your "Quick Mission Builder." Does it take you to the set-up menu? Can you begin the mission?
Once you are happy that everything works in your clean Il-2 game, then install VP Modpack on top of it. I do not know of any problems of VP Mod breaking anything so what works in your clean game should work again after installing VP Mod.
Let's first get your base VP Mod running before considering the expansion. The expansions add contents such as maps to the game, but if your game is not working before adding the patches, then it unlikely to work after the patches are installed.
Aerobatix - what you describe sounds like how your computer is displaying the files, not a problem with the file themselves. Open file explorer to the folder with your VP Modpack files. Using file explorer menu at the top, click on "View" Under "Layout" click on "Detail." It sounds to me that you are viewing your files as "Icons" which displays your files in rows. "Detail" layout displays your files in a column as shown on the examples within the forum thread. Detail view also provides information about the file such as its size. The blank white boxes is telling you that Windows has not associated them to a program on your computer. If you double-click on any of the files, a windows menu pops up and asks you what program you would like to open it with. That is why you right-click on the first file. Right clicking opens a windows menu that displays a whole list of options you can do with the file such as "open with" and in our case "7-zip."