Bravo... thank's.
csvousden... listing the contents off the setup's would be fairly long, as for say the IL-2 1946 4.09m Poland Finland USSR Early War mod folder which has 166 mods in it at this time.
The first item I would have to say is that "order" is the best start for any modded game setup, do it in small, one at the time steps. Also I open for say my mod patches, the game object page, mod folder page and the game main page all at once. This removes some of the chance of error and having to search around and then do one really important item that you'll need to do and offen... is to back up everything! LoL
Start with a blank setup of 4.09m and make a copy... use the copy for making the first running game with all of the nonaircraft mods already added and have this game running with no problems. Then use a copy of this setup to make your other games by adding in aircraft, maps and etc depending on what you plan to use this game for or what theater of the war you what it for.
Here is a screen of my IL-2 patch folder below... on this drive which has none modded games, mods and skins more or less, there are 931 GB being taken up on the HD and the most space is being taken up by just the mod folders. This setup for the patches allows me to just go to the mod I need more or less without spending time searching all over for it. But you will need HD space... I have three external drives at this time.