I doubt very seriously that you will find anything published or from software that can get you above and beyond factory specs. Most aftermarket research is trial and error combined with experience on a dyno. All of the data is closely held. After all thats how they make money, I know, I ground two stroke cylinders for about 5 years.
Port size, as I previously mentioned, is limited to what keeps the top ring from diving into the port. Port shape and flow direction plays a large roll, but with each set of cylinders you are limited with what what you have to work with from the factory. Basic port timing is fairly standard stuff with some room to play around with. You can get fancey with transfer port timing by allowing some to open sooner than others yeilding different flow patterns across the plug.