Hi Jimmy.
The firmware will not have an impact on the array, it should boot fine regardless of the current setup (with the specific exception of RAID6).
If I remember correctly, the 1.1x or 1.2x firmware came on my last replacement board a couple of years back (I run 2008R2 and CEntOS 5) and only had to upgrade from the OS.
Install the replacement controller, boot to OS, Upgrade the firmware, and see what the ACU reports.
Cheers
Leon