OBIO, I don't know anything for the autogen trees, but usually people use Lumberjack utility to remove those at the end of a runway.
Concerning the clouds, you have two choices:
- the most famous is the HDE package from Pablo Diaz. It was made for FS9, but the cloud textures will work with FSX. The sky textures will NOT work, but there is an alternative package made by somebody who converted Pablo's sky textures to make them FSX compatible. Search on flightsim.com or avsim.com, using Pablo's name.
- the other alternative for clouds is to use FS SkyWorld 2004, which was also made for FS9. Just like Pablo's package, the sky textures will not work, so don't try to install them. The cumulus textures will work fine, but you'll have to use the FS Skyworld installer, don't try to transfer the texture files directly, they are not in the correct format (the installer modifies them, just tell it to install in a dummy folder). Compared to HDE clouds, the resolution is smaller (and easier with FPS, but still beautiful), but you have much more choice (HDE has only one set of clouds).
Remember, DO NOT INSTALL THE SKY TEXTURES, ONLY THE CLOUDS.