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The Yuan-Tseh Lee Array for Microwave Background Anisotropy (AMiBA) is a co-planar interferometer array operating at a wavelength of 3 mm to measure the Sunyaev-Zel'dovich effect (SZE) of galaxy clusters at arcminute scales. The first phase of operation-with a compact 7-element array with 0.6 m antennas (AMiBA-7)-observed six clusters at angular scales from 5^′ to 23^′. Here, we describe the expansion of AMiBA to a 13-element array with 1.2 m antennas (AMiBA-13), its subsequent commissioning, and cluster SZE observing program. The most noticeable changes compared to AMiBA-7 are (1) array re-configuration with baselines ranging from 1.4 m to 4.8 m, allowing us to sample structures between 2^′ and 10^′, (2) 13 new lightweight carbon-fiber-reinforced plastic (CFRP) 1.2 m reflectors, and (3) additional correlators and six new receivers. Since the reflectors are co-mounted on and distributed over the entire six-meter CFRP platform, a refined hexapod pointing error model and phase error correction scheme have been developed for AMiBA-13. These effects-entirely negligible for the earlier central close-packed AMiBA-7 configuration-can lead to additional geometrical delays during observations. Our correction scheme recovers at least 80 ± 5% of the point-source fluxes. We, therefore, apply an upward correcting factor of 1.25 to our visibilities to correct for phase decoherence, and a ±5% systematic uncertainty is added in quadrature with our statistical errors. We demonstrate the absence of further systematics with a noise level consistent with zero in stacked uv-visibilities. From the AMiBA-13 SZE observing program, we present here maps of a subset of 12 clusters with signal-to-noise ratios above five. We demonstrate combining AMiBA-7 with AMiBA-13 observations on Abell 1689, by jointly fitting their data to a generalized Navarro-Frenk-White model. Our cylindrically integrated Compton-y values for five radii are consistent with results from the Berkeley-Illinois-Maryland Array, the Owens Valley Radio Observatory, the Sunyaev-Zel'dovich Array, and the Planck Observatory. We also report the first targeted SZE detection toward the optically selected cluster RCS J1447+0828, and we demonstrate the ability of AMiBA SZE data to serve as a proxy for the total cluster mass. Finally, we show that our AMiBA-SZE derived cluster masses are consistent with recent lensing mass measurements in the literature.