CC,
The 6537 is only capable of a 50MHz clock rate. If you need to interface at 100MHz then I would suggest looking at the 6542 or the 6552.
Also, if you are capturing only 14bits of data, then you can gain the throughput benefits by selecting the correct pin mapping. You should have no trouble sustaining a 50MHz interface rate with 14bits provided you keep the channels mapped to two ports.
In response to your questions, PFI5 is a source synchronous clock input. The default populated 0ohm resistor is necessary since this is a series element. It was made optional to allow users to replace it with a 50ohm series termination for those applications where the CB 2162 is used as a prototype platform and the driver is very near to the connector. If you are cabling to the connector then you should leave it as 0ohms.
Futhermore, it is a synchronous datapath. That is, the traces and cabling are matched between all of the data and pfi (clocks). The 6537 does require some setup and hold time relative to the clock you are inputing to PFI 5. These can be found on page 9 in the specifications:
http://digital.ni.com/manuals.nsf/websearch/906B148A0F455765862573690041C6BE
2ns of setup required
2ns of hold required
You can alternately use the data position attributes to sample the data on the falling edge of the clock. This may provide sufficient margin to both setup and hold.
In regards to the "bad" waveform. Keep in mind that if you have the 2162 connected up to the 6537, you will be probing in the middle of a transmission line so you will see a reflection. Depending on the source impedance of your driver and the impedance of your interconnect to PFI 5, these reflections may persist. the 2162 and the 6537 cable are designed for 50ohm matched impedance. the interconnect and driver should match these characteristics. If they are matched, then probing in the middle of a transmission line will show a stair step in your waveform. Try running at some slow speed (5MHz) and let the reflections settle out. The 2162 and cable have about a 5 to 6 ns propagation delay so you should see a step on the order of 11ns if you probe at the resistor on the 2162 (assuming your interconnect is well matched). If your waveform is a departure from this, please attach a screenshot and a detailed explanation of your system interconnect.