Two of the boards in a can (reference and plug into the motherboard with 37 pin DIN connectors. I ordered a couple of cables. That should allow me to run it out of the box, so to speak.
I pulled all the units and plugged them back in. Voila', the dang thing gives a decent output wave below 500Mhz. The output of the 10mhz reference board is still crappy, but not jittery anymore.
Above 500Mhz, there is now a AM modulation on the output, but no jitters.

The reference board creates 10Mhz and 1 Mhz signals (for PLL Phase detection), and has another PLL on it that uses the 1 mh to make 512 Mhz for the mixer on the output board.
When I tapped on the DDS board the RF output signal got brighter on the scope. Something loose and creating a resistance on the output or references? I think I need to check the motherboard out carefully.
Oh, Hell. I was wondering why the card and slot position diagrams did not match up with what I was seeing. The top board in lower right can is the Reference/Lo board. And that is all they show on the diagrams. But there is another card in there. I finally got it into my head to run all over the manual and found out it is a deviation meter option. I am still a basic noob, but I hope this is a useful option.
sheesh. I have been reading and studying so much to try to understand this thing, only for it to come and hit me with something else to learn.