First off whatever happens you will get machining marks. The only way to finish your blocks base on a machine is to gind it but unfortunatly copper is too soft to gind easly (and im guessing you dont have a surface grinder to hand)
The alinement of the head wont relly make alot of differance to surface finish aslong as its within normal tolorances (if its not then your going to be cutting a concave base anyway so its still important as ever)
The way you clocked up on the quill is a pretty bad way of doing it. A better way is to get yourself a bit of rod about 6" long, put 90deg bend on each end in oppisite directions. Then attach your indicator on one end and hold the other in the chuck (you can buy something simlar but its easyer to make). Take the mill out of gear and swing the indicator around on the bed 180deg checking the dial stays the same.
Try bull nose inserts but what ever you do your still going to have to lap it
slater..