Stoney, it's not the size of the clouds that reduces framerates, it's the quantity.
If you keep in mind that the total number of clouds generated at any one time is 900 or less, you will have no problems. That's right from the Cloudeditor read-me. When you "submit" and "animate" the clouds in the editor, a counter will read out the number of clouds at that moment, with another counter marking the highest number. Use that to determine how many rows/columns to make. Using simple math, you'll realize that a 30 by 30 row/column cloud bank will give you 900 right there, so be careful how you add up multiple banks.
By using fewer but larger clouds you will find that you can cover quite a bit of terrain and still be under budget with the total cloud count.
Don't try to cover the entire terrain with clouds; only cover where you think the major action will be.
Denholm I can't imagine what you must have done to get 4 fps.