The first thing that would be best to do would be to connect a serial cable to the failing controller and use PuTTY to enable output logging and boot the array up. All the output from the controller will be put in the txt file you setup and that will tell us more exactly what is causing the fault.  When it comes to replacing the controller with a controller with Gen 1 FW, it will take longer as it syncs the firmware load and reboots about 3 different times. I would also recommend that you connect the serial cable and enable logging for this process as well to ensure that everything goes as it should.
We own an MD3000i with two active RAID controllers.  Both controllers are running ‘gen 2’ firmware.  Recently, one controller began failing (after booting the MD3000i, network ports come up, then about 5 minutes later management port and iSCSI ports go ‘dead’..no link lights.)  We have a spare controller and have tried swapping it in, but the alarm light is on and network ports don’t come up.  I’ve tested the spare controller in another MD3000i chassis and confirmed that the spare controller has ‘gen 1’ firmware and that the management port and iSCSI ports work fine.  According to this document (written specifically for an MD3000) the controller may take up to 30 minutes to sync firmware and come up properly: [URL]  A few questions: - should we try swapping in the spare controller and give it more time to do its voodoo? - does it matter that the spare is ‘gen 1’ firmware, will a sync update this to the ‘gen 2’ firmware that’s on the working controller? - does the warning light on the replaced controller indicate anything?  
Swap failed controller in duplex MD3000i