Proably need a bit more info from you as to what you are trying to do, but here goes.
I. Install CFS3 on the new HD from the original CD's.
2. Install the 2 updates.
3. Make a copy of this (copy function) to another place, say your desktop.
4. Re label this copy as, say, "Clean BackUp" , and put it back in C:\Program Files\Microsoft Games\ or your equivalent place. Later if you need more install you can copy this copy and then rename them such as "Combat Flight ETO39toBoB" or what ever you want.
5. Now at least you should have 2 versions of CFS3 in the program folder; Combat Flight Simulator 3 and the clean back up.
6. The nest step depends on what you want to do. If you want to install the ETO expansion then download it and follow instructions. It will automatically make a new install off the CFS3 install. Not much you have to do other than follow the instructions!
If you just want to add your old modded stuff, then I would just copy and paste all the files over to the CFS3 install, bearing in mind that
This will no longer be a clean install for making MAW,PTO, or similar installs. You will have to use the clean back up.
Actually the Martin Wright MultiCFS3.exe is dead easy to use with simple instructions, so you can have as many separate installs as you want or have HD space for!!
Hope that helps.