Do it now. Once you have your cylinders ported for the stock crank they cannot be ported for a 4 mill crank. You will have to get new cylinders and have them ported for the crank. Really all it would cost to do the 4 mill would be the cost of the crank, and a new set of stroker domes for your cool head.
I think jeff sells 4 mill cranks for 400-450.