Eric, that mob custom preparation article is solid. I followed it on two cylinders I modified. I got a 20mph cylinder to ~30mph and a 30mph cylinder to ~40mph following it, both with the stock exhaust and a 15 sha carb. I did a much better/cleaner job porting the slow cylinder then the fast cylinder, and still got stellar results out of the fast jug!
It's a bad idea to try and modify the transfer windows in the cylinder, they are usually angled for the best scavenging results. If you want to increase their timing, raise the entire cylinder up and shave off the top.