I currently have a clean 4.09m installed. I would like to download HSFX but I would like to also keep the clean version (no mods). How do I go about creating both so that can go back and forth?

Create a folder somewhere outside of Program Files. Copy the entire IL2 Sturmovik 46 folder into it. Remember to correct your filepath when installing anything else, remember to rename any desktop shortcut that you create.

Yeah, it's easy, just right-click on the il2 folder, select copy, then go to where you want the new folder at and just right-click and select paste, done.