The second-dimension (2D) temperature programming system (2DTPS) for comprehensive two-dimensional gas chromatography (GC × GC) described in Part 1 was updated and tested with the time-of-flight mass spectrometer (TOFMS) and flow modulator. Addition of a real-time clock and remote port allowed the 2DTPS to be a truly standalone system to be used with any GC × GC instrument. GC × GC reproducibility with the 2DTPS was tested with thermal and flow modulation, coupled with the TOFMS and/or FID to demonstrate compatibility with all typical GC × GC setups. An improvement in the match factor, reverse match factor, and signal-to-noise ratio was found when performing 2D temperature programming. Within-day and day-to-day reproducibility of the 2DTPS for the 1D retention time (≤0.04 and ≤0.05%), 2D retention time (≤0.36 and ≤0.52%), and peak area (≤2.47 and ≤3.37%) were acceptable, while providing flexibility in 2D optimization and improved peak capacity.