A photomultiplier (PMT)-based diagnostic system for monitoring spectral lines along multiple viewchords, named the "Filterscope" [R. J. Colchin et al., Rev. Sci. Instrum. 74, 2068 (2003)], is currently in use at the DIII-D, NSTX, and CDX-U fusion plasma devices in the US, and has been installed at the KSTAR device in Korea. This diagnostic has recently been upgraded for application to long-pulse devices, such as KSTAR, EAST in China, and the future ITER in France. A new data acquisition system, employing the PXI instrumentation platform with an embedded Windows microprocessor controller, can simultaneously record up to 72 channels at 100 kHz sampling rates for plasma periods lasting up to 20 min. Based on the average signal level during an adjustable time interval (100 ms in the present DIII-D implementation), the controller digitally adjusts PMT dynode voltage throughout the course of a discharge, thereby maintaining the output signals at a level where they are neither saturated nor dominated by digitizer noise. The new system's ability to accommodate large variations in source strength, discharge to discharge and within a single discharge, has proved particularly valuable during DIII-D operations, since changes between top, bottom, and double-null divertor magnetic configurations lead to large temporal variations in signal brightness.