Tim,
There are any number of things which might cause you to misunderstimate size of required tank. But a ground run using flying fuel, flying prop and a reasonable needle setting (around 11,500 with an APC 9-4) will get you pretty close.
As to setting tank height I can understand where the details of such has so far escaped you. And you might be testing tank height incorrectly.
A lot of folk simply fly level upright and then inverted to see which way to move the tank. And that's fine, although if the run is good enough to keep the model flying the first time I do this test is pretty much the last time.
The real test comes in maneuvers. Inside and outside loops (big ones at first) will tell you quite a lot as to tank position, as will horizontal 8s. The final test is to fly in a bit of wind, especially with small-bore engines on 400-inch profiles. The wind pretty much turns the model into a kite; this in turn results in more speed and if the tank is even the slightest bit off you will soon be roaring in one direction, slower in the other.
This can catch even the experienced out. I had fitted a new tank to my OTS model (Zilch X, 600-inch model, 25FP, tongue muffler, no pressure, APC 9-4), new tank as I wanted to try this model in Classic. In practice it was bitchen following minor shimming of tank. But at next contest there was some "interesting" wind 1st round and the thing just howled in outsides. Dropping the tank 1/32" cured it of all evil tendencies. And, yes, I confirmed this at next practice session, waiting for the wind to pick up prior to flying this model.
You are correct in establishing a reference for the tank. In my installations there are hooked rods top and bottom of the tank. These serve to hold the tank in place with large "O" rings but the neat trick is the assortment of shims between these rods and tank. In order to change tank position but not have to fiddle with clamping pressure of tank to fuselage one, for example, removes a 1/32" shim from top stack and then adds it to the bottom stack. Easy, consistent and repeatable.
As a final point, use of a clunk tank makes testing pretty easy without doing a whole flight. Get 1 ounce of fuel into the tank, fly a few loops, make required changes.
Dan