Hello,
The NI 5412 does not have a Digital Data Connector (DDC) like the NI 5411 did. The NI 5421 can be purchased with the DDC but the signals are LVDS, which may pose a problem for your current setup.
With the NI 5421 (and NI-FGEN 2.4 or newer) you can route up to 4 Data Marker Events (each one being any bit in your waveform) to any PFI line or RTSI/PXI_Trig line. Additionaly, using Script Mode (also available in NI-FGEN 2.4 or newer) you can route up to four Marker Events to any PFI line or RTSI/PXI_Trig line. Keep in mind both of these advanced features are not available on the NI 5411 nor the NI 5412.
From the sound of your problem, perhaps you should take a look at our High Speed Digital IO line of products.
http://sine.ni.com/nips/cds/view/p/lang/en/nid/12761
Hope this helps.
Marcos
Marcos Kirsch
Chief Software Engineer
NI Driver Software