There is an easy way of getting different high clouds for the same map:
1) Make different copies of the original load.ini of a map, modify and rename them
2) Rename the first line of the .mis files
ex for the MTO map:
MTO_load.ini (if this is the name of your original MTO load.ini)
Copy it and rename it for ex: MTO1_load.ini and change the two lines that will modify the high clouds, for ex hi_CloudsNoise for the first line and then vp_clouds01.tga (from VPmedia's mod) and of course put this new load.ini into your MTO folder.
Do the same if you want more different high clouds for your MTO map, for ex MTO2_load.ini, MTO3_load.ini etc ... and of course modify the two lines, for ex hi_CloudsNoise for the first line and then vp_clouds02.tga etc ...
And of course don't forget to modify the first line of your MTO campaign/missions .mis files (the one that tells the mission which map to load) according to your taste ...
This is rather time consuming but doesn't need a lot of space on your hard disk since the new load.inis will only be a few kilo octets since they are in text format ...