Check out some of YDNAs stuff on zdspb, should help. I usually match the feedneck bore to the body bore, which means the shelf goes away. Also, cutting to the center of the main bore should help, vs a certain distance. I haven't done a ton of full body design though.
I do have an actual feedneck drawn, it's a reverse engineered Etha feedneck. I can post the files after work.