To run longer rods (stroking), you would need to modify your block, so that they don't slam into the side during rotation. You need to raise the compression through the pistons, thinner head gasket, or milling (bad idea since once it is gone, it is gone) the bottom of the head.
Here is a decent link to read up in
http://www.automotiveforums.com/vbulletin/t15933.html
I forget the guesstimation equation for Hp to CR. I want to say it's 10 Hp per point, but I am probably way off.