You can run the bd3 brakes on 5.4, it's the second option. Personally I like the X stock brake (default 5.4) better for stock classes, I think it has enough strength and the lo/hi speed brake balance is better. You might find running 1-2 initial brake with the X stock gives you a better brake feeling.

For the d4, I would start with 4.6 fdr and 50* timing. Adjust gearing to temp/track size.