Installed SQL Server 2000 with wrong collation.. how to correct for entire server instance?
Quite honestly, I think your easiest approach will be:


backup your user databases
uninstall SQL Server
reinstall SQL Server with the right collation
restore your databases
fix the collation on the user databases


Also you know that SQL Server 2000 is well out of mainstream maintenance, right? And that quite soon there will have been FOUR major releases since then?