I've never heard of a perfect brass round. Most test bars are made of hardened, ground steel. It makes for a stiffer test bar to eliminate sag at the end and any marking of the bar from chuck or bumping that would cause false readings. However, for our purposes, it should be fine. When you say that your readings only change a couple of thousandths over the length, just how far is the length? 30 inches and that would be great, 6 inches would be horrible. Yes, truing the faceplate by making a cut across it's face will insure a 90deg. angle between faceplate and bed but only if the headstock spindle is in alignment with the bed. If the headstock is out of alignment then when you face the back plate you are either making it convex or concave depending in which direction the headstock is out.
If the test bar is chucked up at about 12 inches and turns true without the tail stock holding the free end, then your chuck is running true at that opening. I don't know what kind of lathe you are setting up so I don't know your set-up for holding tapered objects such as pool cues. If you have a chuck on the back of the spindle then you need to make that same test but with the bar extended between the two chucks and sticking out around 12 inch again. if it runs true this time and the cut is only a couple of thousands off I would say that it is to little to worry about and assume that the headstock is aligned good enough to the bed. I have my lathe tuned so that it runs less than .002 out at 30 inch. It is hard to get a lathe to run perfect because of wear affecting different parts of the bed in different amounts. Also, it is very hard to get a tail stock properly aligned with the spindle. It's not real difficult to get the tail stock aligned as far as left to right but as far as up and down and being true at both ends of the tail stocks movement is much more difficult. Often, this is where the trouble is and few people look in this area. Often a tail stock is made to be two or 3 thousandths high, to help account for wear over the lathes useful life.
Here is one place to get some information on the proper way to set up a lathe. There are many others on the net but I don't have their links handy.
Dick
http://metalworking.com/tutorials/ARMY-TC-9-524/9-524-index.html