Put those mods that you arent using in another folder somewhere else, and then when you want to use them drag them to you mods folder. Takes much longer when it has to load all the mods even though your not even using them.
Other than that...just try to keep your comp fast, de-fragging, or was it fragging your HD, dont fill the HD to the brim.
Ohyea, and having a no-cd image makes the whole process faster in the terms of getting the cd, inserting it and waiting for it to load. you can get it at
www.core-clan.com