Stroking a RS125

[GP125_Racer]

I am in the process of stroking an 2000 Honda RS125. The stroke has been increase 4mm, and I am using a 5mm longer rod. How do I determine how much to raise the ports? is it as simple as keeping the same degrees? If I keep the same degrees the piston goes below the ports, should I increase the port size so teh port bottom is parallel withj the top of the piston at BDC?

Also,what effect does shortening and lengthing the exhaust blowdown have on performance?