Manually Uninstall SQL Server Instances

Scenario:
Active/Active Cluster:
3 Instances: Default and Named Instance 1 are sql 2000 and Named Instance 2 is on SQL 2005
Requirement:
Need to Un Install SQL 2k [Default and Named Instance 1]
Final Look:
You should have only named instance 2 [SQL 2k5]
Problems:

1) It looks like sql server 2000 and sql server 2005 have a common binn files on both the nodes i.e. on D:\mssql\

Backup Taken:

1) Copied Binn folder to the new location
2) All user database backups on SQL 2k5 named instance and also configure the T-log backups for all the database for point in time recovery.
3) MSDB database backup on SQL 2k5 named instance
4) Login Script [optional - take the script of Jobs/Linked Servers]
5) Dropped the SQL Server 2000 cluster resources from the cluadmin as this would stop the alerts [but still the sql server2000 instances remains]

Used the following KB article to uninstall SQL server instance manually

http://support.microsoft.com/kb/290991

We have referenced below kb article to remove the SQL Server from the server:

Plan 1:
1. It looks like sql server 2000 and sql server 2005 have a common binnfiles on both the nodes ie. on D:\mssql\
2. Incase if we follow the below article would there be any issuesfor exitsing 2005 instace ?
http://support.microsoft.com/kb/290991
Other work around would be to drop the SQL Server 2000 cluster resources from the cluadmin this would stop the alerts but still the sql server2000 instances remains.

Plan 2:
We can take a total backup of d:\mssql folder on both thedrives and take down time on all the 3 instances rename the existsing mssql-oldfold

Plan 2 worked for me :), before proceeding with this please be ensure that you have taken the full backup of your databases.