I know that the driver for gen2 Avalon needs to subtract 0x180 from the returned nonce but are there any other changes?
There was a limitation (999 MHz) for the command-line parameter for the desired chip-frequency in some versions of cgminer - That has to be removed or changed to 5000 or so.
Thats the only thing that has to be changed, additionaly to the 0x180 substraction (which BFGminer detects automatically).