Free Space Optical (FSO) Communications channels can exhibit high percentage availability, yet are subject to frequent intensity fades due to turbulence effects. For gigabit class links, tremendous amounts of data can still be transported through a fading channel, but an efficient network protocol is required to overcome the effects of fades. We describe a custom error detector that can process a digital signal from a channel which has frequent fades below system sensitivity and can provide data link statistics with bit-level timing accuracy. The statistics measured by the instrument include bit level counters that allow the device to be used as a traditional bit error rate tester (BERT), as well as block-based counters, which provide insight to the channel for packet based transmission formats. Synchronization parameters are adjustable to accommodate different link dynamics. Additionally, stretched error and sync pulse outputs provide useful live indicators of link performance when plotted against optical channel power. This paper will discuss the performance of the custom bit error rate tester (cBERT) in testing a 2.5 Gbps channel over a maritime FSO link trial conducted off the mid-Atlantic coast near Wallops Island, VA, in July and September 2009. Additionally, the overall design of the cBERT will be presented.