Thanks for the response Larry. I'm afraid I have only just come back to this project, hence the delay.
TP16: 1.20 V
JP16: 3.6 V 10.42 MHz square wave (this seems low?! 250MHz / 24)
J5, J8 I see nothing through the small amount of noise.
JP5 and JP6 I've attached images from the scope below.
TP1: 1.84V
TP3: 1.84V
TP5: 3.34V
TP7: 3.33V
TP9: 3.31V
TP11: 4.96V
JP5:~1.9MHz
JP6: ~1.3MHz
So it seems there are two problems:
Problem 1: The clock is being divided by 24 rather than bypassed.
Is this likely to be my error using the SPI software? Are there any tricks to using it?
I can power down DAC1 and DAC2 using the 'Power Down' tab for example, however using the 'AD9516-DAC Clock' tab, neither of the Bypass checkboxes seem to have any effect.
For my purposes, I don't ever expect to need the AD9516. Would it be reasonable to switch JP2 and JP3 to connect to J4 and use that as a direct clock input? If so, is there anything I need to do to disable AD9516?
Problem 2: The output is shown at JP5 and JP6 but not J5 and J9.
I don't have a multimeter today and will have to wait for Monday if I need it. However it should be possible to figure this out from the schematic. I would expect (for example let's look at DAC1) that JP4 and JP5 be connected between 'Com' and 'B', to send the output through T5 and T7 to J5. On my board they are connected to 'A' which looks like it goes to the modulator output (however I still see nothing at the modulator output).
Should I just change the soldering on JP4, JP5, JP6, JP7? Is anything else necessary? I wonder if this error occurred only on my board.
One final observation when I looked closely: in the schematic R40 is connected to J8, and R41 to J9. These are reversed on my board, although I keep confusing myself with polarities trying to figure out which one is wrong, so I'll leave that for now!
Anyway, thanks for advising me what to look at. If you could let me know about the clock input, and confirm I can switch JP4-7 to get direct SMA outputs, I'll mark this as Answered!