A method for assembling a stackable perforating gun system inside a well bore is provided that includes attaching a first gun section of the stackable perforating gun system to a tracking assembly, and transporting the first gun section within the well bore using the tracking assembly. The method also includes disengaging the first gun section from the tracking assembly; retrieving the tracking assembly to the surface; attaching a second gun section of the stackable perforating gun system to the tracking assembly; transporting the second gun section within the well bore using the tracking assembly; and coupling the second gun section with the first gun section using the tracking assembly.