Why doesn't velocity enter into Heisenberg's Uncertainty Principle?
Some problems with your method: you mention taking 100 copies of the same atom of hydrogen and finding the positions at 100 different times. (i) You actually can't make a copy of a quantum system without knowing its quantum state (the no-cloning theorem), (ii) your measurements of position will disturb the "trajectory" of the electron, so your 100 cases are distinct and cannot represent the path of a single electron, and this is especially true the more accurate you make your measurements.

You should realize, however, that the bound placed by the Heisenberg uncertainty principle is really quite small, and on a macroscopic scale we can essentially determine the trajectory of an electron. A bubble chamber or cloud chamber is essentially a major revision of your proposed method: we fill a vessel with supersaturated vapor, wait for charged ions to pass through the vapor and cause it to condense, and observe the resulting tracks. This describes the ion's motion with a resolution on the order of microns.