The only supported way to clone a system is with sysprep. There are a bunch of reason why not to clone a sql server:
-Its not supported by Microsoft CSS.
-SQL will not work properly until it is "renamed".
-If you have reporting services it will be hosed as well.
-The System and Network Service accounts will get new SID and passwords, so if you have used these as service accounts there will be some pain.
-SQL Server creates a good few local groups with the format. SQLServer2005MSSQLUser$$MSSQLSERVER. Its not supported to rename these
In order to rectify the situation I would-
Break the cluster, rebuild the system, install SQL, create a new cluster, run a backup on the server that's not been rebuilt- then stop it, restore that backup to the new cluster, point the application to the new cluster, rebuild the remaining server and add it to the new cluster
-- alternatively (probably easier) why not build a new server with new name(this will solve potential issues with SID of any type) then break the cluster install SQL join it to the cluster, failover to that box then repeat the process, that way no downtime and no need for backup/restore (although I would suggest you did though anyway). We use zznode1, zznode2 and a cluster name that way creating zznode3 and joining it to the cluster is simple as the node is not referenced when in the cluster. Hope that helps.