My experience with the Graham fixtures for arm position and cart alignment was initially very trying. I have the 9" arm. To begin, arm position needs to be such that the spindle locator pin has no stress from any direction when the headshell receptacle is lowered or raised over it. Had to get some longer 4-40 cap screws and over-drill the arm-board to make that work on my Sota. After many hours of frustration trying to get the cart alignment right, I finally realized I needed to make a macro-fixture that would hold the entire arm/cart/alignment fixture assembly stable during the adjustment process while allowing free access to all the fasteners. Only then could I fiddle around with the alignment jig targeting reticle height to get it parallel to the cartridge body and arm. Getting the stylus alignment spot-on took a stereo zoom microscope at about 15 or 20x. The vertical weight issue on alignment is a red herring IMO; the arm is inverted when using the reticle and you will be adjusting VTA (or more precisely, as Doug would point out, SRA). Any deflection caused by differing weight is not realistically measurable. Double-checked with my Pro-Ject protractor, and it was dead on. Once all that was accomplished, setting the VTF, VTA, azimuth and anti-skate was a breeze. Very minor adjustments became clearly audible and I quickly got it dialed in to my taste.
Be advised that patience is essential. The whole process took me nearly 3 MONTHS. Much of that was due to the fact I live in the sticks and have to mail order everything, including things like washers and 4-40 socket head shouldered cap screws. I also encountered several unrelated failures along the way. Still, even if I'd had no failures, lived in a city and picked up all the stuff I needed in one trip, it would have taken a week or more. Ah, the joys of such a fussy, exacting hobby. Just rest assured it will all be worth it - the Phantom Supreme II is a marvelous arm.
Good luck & happy listening!