As this is quite an old thread I expect you've got your cluster issue sorted now (or given up ;-)), but I've recently been doing the same thing.
I didn't need to take the drastic steps that SK recommends - there's no need - but you need to make sure that when you start SQL Server in master-recovery mode (using the /f and /T3068 parameters), you run an ALTER DATABASE command to logically MOVE the mssqlsystemresource data and log files to the new location and then physically move the files.
You should then be able be able to change the startup parameters in SQL Server Configuration manager and restart the SQL Server Service via Cluster Administrator. If that doesn't work, copy the master and mssqlsystemresource data and log files back to their original location, start SQL Server (via Cluster Admin), make the changes again, shut down SQL Server (again via Cluster Admin) and restart. The new startup parameters should then be picked up.
This problem is caused by Registry entries on the cluster getting out of synch with the startup parameters. I can testify that it can be a complete pain!