changing the port number for a sql server cluster should be a pretty straight forward task.  Most Clustered sql servers will be mission critical, hence the clustering; this also means it will be properly secured behind a firewall.  This means you will need to run the SQL Server instance on a static port.  In some instances you can not choose the port that SQL chooses for you.  In these instances you will need to change the port number for SQL Server.

There are several resources out there on how to do this (why Microsoft didn't make choosing this as part of the install, or an option in cluster manager ), but all of them referenced using a command line program "Cluster Res", unfortunately this errors out on Windows 2008 R2 and SQL 2008 (r2 as well), with a "can not find the file specified".

For Windows 2008 R2 and SQL 2008 you need to run "Cluster . Resource" from the command line.

The basic directions are:

1.  Take the SQL Server instance off line.

2.  cluster . resource "SQL Server (<InstanceName>)" /removecheckpoints:"HKEY_LOCAL_MACHINE\Software\Microsoft\Microsoft SQL Server\MSSQL.x\MSSQLSERVER"

3.  Open SQL Server Configuration Manager (ensure to "Run as Administrator"), Make the appropriate changes.

4.  cluster . resource "SQL Server (<InstanceName>)" /addcheckpoints:"HKEY_LOCAL_MACHINE\Software\Microsoft\Microsoft SQL Server\MSSQL.x\MSSQLSERVER"

5.  Bring the SQL Server Instance back on line

6.  Verify in the sql server error log that the instance is using the correct port.

Easy stuff, that Microsoft should have made easier.

How to change SQL Server parameters in a clustered environment when SQL Server is not online (http://support.microsoft.com/kb/953504)

http://sqlserverpedia.com/blog/sql-server-bloggers/sql-server-configuration-time-bombs/