[I am relaying information from Vijay here, my free interpretation]
An S series board should be used as the primary board. The board tested and benchmarked in the article (2003) is NI PCI-6110, a 12-Bit, 5 MS/s/channel DAQ board. This is a PCI-card and supports the rates need for input digitiazation (1.25MHz).
ScanImage 3.7 can also use X series cards (e.g. PCIe-6321 or 6323) with DAQmx 9.2.2. (http://www.ni.com/xseries/). These PCIexpress cards can be used as the optional second board for Pockels cell control and/or to have full frame/line/pixel clock features.
possible faster and more expensive alternative for the main card?
Is PCIe-6361 the card that can do it all?
According to http://sine.ni.com/ds/app/doc/p/id/ds-151/lang/en, this card could output 2 channels at 2MS/s each and sample a single channel at 2MS/s, and multichannel at aggregate 1MS/s.