Just an update in case somebody going through the same process stumbles on this thread...
The WiSM to WiSM2 upgrade went very smoothly. I was able to backup the WiSM config, install the WiSM2 and restore that config to it. Cisco even has an updated deployment guide with steps for upgrading from WiSM to WiSM2 where they recommend this process. http://www.cisco.com/en/US/products/hw/ ... 2500.shtml
After performing the upgrade and restoring the WiSM config to the WiSM2, I ran a config audit in Cisco NCS. It complained about the hardware change and recommended removing the controller from NCS and adding it back. I did that, ran another audit, refreshed NCS config from the controller, and everything was good. It was actually a pretty simple process.
As mentioned before I upgraded the ROMMON, Flash memory (with the compact flash adapter), and IOS on the 6509. With dual sups, the only downtime I had was the minute or so failover time from one sup to the other when they were on different IOS versions. I did not update the firmware on any line cards and that never came up in any discussions with Cisco TAC.