i'm in the middle of build'n my first 4 link also. i'm shoot'n for 4" verticle seperation at the chassis and at least 8 or 9 at the axle. as far as link placement on the chassis i think most of it is determined by what works for your particular application, then once you get an idea on that it will help you at the axle based on clearances on the moter, drive shafts, tires, etc. on the front my lowers will have a lttle more triangulation than the uppers to avoid contact with the engine.
you can plug the "perfect" numbers into the calc. but that may not work for you.
like i said, i'm no pro, obviously a rookie too but this is the way i'm going about it at the moment. i've seen plenty of rigs that look like **** was just thrown on and they seem to work, but i'd like to dial mine in a little better than that.