The error you received is generally due to the ROMB dimm failing, not the controller. What you can do is power down the system and then remove the ROMB battery cable to the controller, then reseat the dimm, then restore the battery. If that doesn't work you can remove battery and dimm and then install dimm in the memory slot for the server (with other dimms removed) and see if the dimm recognizes, that will tell us if the dimm is failed. If so you may just need to replace the dimm and nothing else.
**NOTE: The ROMB battery MUST be removed prior to insertingthe ROMB dimm, as it makes the slot powered and can damage the dimm if installed.***
With the move over to the PCI-x controller, the process should work. If you pull the config from the drives the locations won't matter as it will know what drive goes where in the array.
Let me know how it goes.