shouldnt the farthest port be beneficial with a slanted master cylinder as air wants to rise to the top and that is the top of the cylinder when mounted.

I guess my question is "why did you bleed the MC" (was it a new one, or did you have some sponginess you were troubleshooting?). If it's new, you may not have gotten all the air out of one of the ports - bench bleeding can take a long time sometimes; and if it's old, the MC seals could be kaputt.

Either way, you'll need to bleed the lines once you open the system.