Dead rock doesn't make cyano. It isn't the cause. As you mentioned, the lack of bacterial diversity sounds like a major contributing factor which is not helped by removing rock that has been curing for 6 months.
Rock being a detritus trap is another thing completely with many ways to get around.
You can add Flow into your macro chamber to help with the sheeting cyano.
I'd still be coming down on the side of Adding quality rock or rock rubble to the system vs removing previously inert rock.
I practice what I preech.