Differential pigmentation between phytoplankton allows use of fluorescence excitation spectroscopy for the discrimination and classification of different taxa. Here, we describe the design and performance of a fluorescence imaging photometer that exploits taxonomic differences for discrimination and classification. The fluorescence imaging photometer works by illuminating individual phytoplankton cells through an asynchronous spinning filter wheel, which produces bar code-like streaks in a fluorescence image. A filter position is covered with an opaque filter to create a reference dark position in the filter wheel rotation that is used to match each fluorescence streak with the corresponding filter. Fluorescence intensities of the imaged streaks are then analyzed for the purpose of spectral analysis, which allows taxonomic classification of the organism that produced the streaks. The theoretical performance and signal-to-noise ratio (SNR) specifications of these MOEs are described in Part I of this series. This report describes optical layout, flow cell design, magnification, depth of field, constraints on filter wheel and flow velocities, procedures for blank subtraction and flat-field correction, the measurement scheme of the instrument, and measurement of SNR as a measurement of filter wheel frequency. This is followed by an analysis of the sources of variance in measurements made by the photometer on the coccolithophore Emiliania huxleyi. We conclude that the SNR of E. huxleyi measurements is not limited by the sensitivity or noise attributes of the measurement system, but by dynamics in the fluorescence efficiency of the E. huxleyi cells. Even so, the minimum SNR requirements given in Part I for the instrument are met.