The first 5 on that site seem to be about having BETTER clouds. Not having FS9, though, I didn't check them out.
Real Edge Cloud pack 1 - Real Edge Clouds Pack 1, includes a set of 5 very realistic clouds with shading edge.
Real Edge Cloud pack 2 - Real Edge Clouds Pack 2, includes a set of 5 very realistic clouds with shading edge.
Real Sky Clouds - FS9 clouds with improved contrast and recoloured for a realistic sky-scape. Pristine high-altitude clouds, golden sunsets, clear dawns, brooding overcasts and moody thunderstorms. No framerate impact because of small texture size (86kB). Extensively tested with no apparent issues.
Cirrus Clouds - The cirrus clouds have been fixed to blend near mountain and remove the hard edge, also fix the intense hard strait cumulus bottom. This files contains good visual quality and good performance clouds performance available for FS2004.
PS Sky - A compilation of the best textures edited by several authors of all the world. The attempt is to offer a product that upgrade the realism of the sky: variations of lights and colors during day and night, clouds with glares and transparency, sun with dazzle effect, moon at high definition, real mapping of stars. Over 170+ textures have been collected to create a more realistic experience.
As best as I can tell, there isn't any
free solutions to your problem in so far as FS9 is concerned.
Just to see how much is possible, you could check out the
Active Sky Evolution trial. You would probably want to rig up a temporary internet access for the trial period.
The lowest cost "weather" that I saw for FS9 is
AFS Design - Sky & Cloud - $12.95.
One part of the problem is the "age" of your flight sim - it was designed to push the computer
of its day to the limit. Adding more would have been useless, so they didn't design the program for it.