Don't modify the Cleanup Script - things in /System are NOT guaranteed to not be deleted or changed by Software Update.
Instead, make your own startup item in /Library/StartupItems
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sudo mkdir /Library/StartupItems/CacheCleaner
You may have to create /Library/StartupItems - I don't remember if OS X ships with an empty one by default or not. If you do have to create it, remember that there is not a space between Startup and Items
Create /Library/StartupItems/CacheCleaner/CacheCleaner with the following contents:
# Start mail server
ConsoleMessage 'Cleaning System Cache Files'
rm -fr /System/Library/Caches/*
rm -fr /Library/Caches/*
Don't forget to chmod 755 /Library/StartupItems/CacheCleaner/CacheCleaner or the startup item won't load.
Now create /Library/StartupItems/CacheCleaner/StartupParameters.plist with the following contents:
Description = 'Cache Cleaner';
Provides = ('CleanCache');
Requires = ('Cleanup');
Uses = ('Cleanup');
Preference = 'None';
OrderPreference = 'Early';
start = 'Cleaning System Cache Files';
stop = 'Cleaning System Cache Files';
This way you don't have to worry about system updates (like Jaguar) trashing your startup item. The line Requires = ('Cleanup'); will tell OS X to run your startup item some time after the standard Cleanup startup item.
Now to clean your personal caches, you're better off using an applescript that launches during login.
Open Script Editor, and put the following lines into a new script:
do shell script 'rm -rf ~/Library/Preferences/Explorer/Download*Cache'
do shell script 'rm -rf ~/Library/Caches/*'
-- Uncomment the next line if you want to nuke your IE History as well
-- do shell script 'rm -rf ~/Library/Preferences/Explorer/History.html'
Save the script somewhere, then go into the Login pane of System Preferences and add the new script to your login items.