Only the OOB's should affect how the mega campaigns work. If you keep a copy of your various versions of the OOB's in seperate directories you should be able to play the various Mega Campaigns with the mech.exe of version 8.2 or 7.1 or 5.0.
The best idea is to install the OOB's from v5.0 for desert fox and 7.1 for the LV and WT MC's.
Screaming Eagles works with version 8.2
So you only need to have three sets of OOB's saved in seperate directories.
Now, to play Desert Fox, copy your v5 OOB's to the main folder and overwrite the OOB's that are there already. When you finish playing and decide to play for example Watchtower, copy the version 7.1 OOB's to the main directory and continue playing.
Then to play your pbem in version 8.2, copy the v8.2 OOB's to the main directory.
So long as your OOB directories remain unedited or compromised, your PBEM and Mega campaign experiences will not be upset.
They struggled with a ferocity that was to be expected of brave men fighting with forlorn hope against an enemy who had the advantage of position......knowing that courage was the one thing that would save them.
Julius Caesar, 57 BC