The effect of varying parameters specific to laser pulse shaping instruments on resulting fidelities for the ACNOT1, NOT2, and Hadamard2 quantum logic gates are studied for the diatomic molecule 12C16O. These parameters include varying the frequency resolution, adjusting the number of frequency components and also varying the amplitude and phase at each frequency component. A time domain analytic form of the original discretized frequency domain laser pulse function is derived, providing a useful means to infer the resulting pulse shape through variations to the aforementioned parameters. We show that amplitude variation at each frequency component is a crucial requirement for optimal laser pulse shaping, whereas phase variation provides minimal contribution. We also show that high fidelity laser pulses are dependent upon the frequency resolution and increasing the number of frequency components provides only a small incremental improvement to quantum gatefidelity. Analysis through use of the pulse area theorem confirms the resulting population dynamics for one or two frequency high fidelity laser pulses and implies similar dynamics for more complex laser pulse shapes. The ability to produce high fidelity laser pulses that provide both population control and global phase alignment is attributed greatly to the natural evolution phase alignment of the qubits involved within the quantum logic gate operation.