Dear Sir,
As far as the first question is concerned, by looking at the firmware source code you will be able to modify the reference source code to have an "continuous" acquisition mode, you send a trigger and you get nsamples * nbursts in the FIFO. This is not implemented so you will need to implement that on your side; SDs, CDs and source code should have enough information so you can carry this task on.
About the second one, in the reference design we set the clock to 122.88MHz, yielding into a 368.64MHz.
I hope that helps,
Arnaud