You can't run the reinstall process when the original is still active in the system registry. Temporarily rename the original install folder to "whatever". Copy it whole and paste the new next to the original. Now you have two installs side by side. Rename the original back to its exact original title and rename the new copy as "CFS2 Vietnam" or whatever. After you rename the new install folder, find the CFS2.exe file inside it and make a shortcut of it to the desktop. Name the shortcut as the theme of the new, ala "CFS2 Vietnam".
That's all the light work. The hard part is customizing by removing the unneeded WW2 planes and ships and installing a lot of the modern era items. Don't worry about removing the stock scenery for now, since the stock bases are all mid and SW Pacific and you'll never see them as long as you're busy in Southeast Asia. After you traverse the learning curve a bit more, you can delve into the process of removing these bases.