[El Gato]

They also don't know the exact mass of the spacecraft - there may be residual fuel onboard that wasn't used but isn't accounted for in the mass calculation.

The mass of the spacecraft doesn't matter. All objects are accellerated the same amount, by gravity that is, regardless of their mass. This is due to the gravitational mass being the same as the inertial mass.... Or is it? Perhaps at very low gravitational strength values they are not quite the same..quantum effects perhaps?

[RandyRep]

The equation for gravitational attraction is something like G * M1 * M2 /(R * R) where G is the gravitational constant, M1 is the mass of one body, M2 is the mass of a second body, and R is the distance between them. Assuming M1 is the spacecraft, M2 is our sun and R is a light year or two, the variable that is most likely to affect the calculation is the mass of the spacecraft.

The acceleration due to gravity of a small mass toward a large mass can be calculated, and is 32.17405 ft/sec-sec at sea level (average) on Earth. The small body moves toward the large body and the large body hardly moves at all (when a rock falls down, the earth would fall up toward it if the rock was large enough).

As stated before, my view is that the value of G is not known with sufficient accuracy and errors of 6 mph out of 10 billion are bound to happen.