Most 6 bolt swaps will have this problem. The black top CAS is less likely to have this problem. The best way to rid yourself of this problem is by using DSMlink to disable the check for random misfires.
Although the problem should clear itself once you shut off the car and restart it, its really not that bad. Although I dont have to deal with it, having DSMLink and all

But yes, even if you use a 2g head on the 6 bolt bottom end, you have to use the 1g CAS, seeings as the 6 bolt block doesnt have the provisions for a crank angle sensor.