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It is perfectly acceptable to use a microcontroller with the LMH0030 and LMH0031 (an FPGA is not required).
For toggling ACLK, one toggle of the clock means one complete sequence of a high transition followed by a low transition. So three toggles of ACLK is: 1-0, 1-0, 1-0.
ACLK controls the data flow through the ancillary and data control port, and there is no low frequency limit for ACLK when it is being used for control register access.
Gary Melchior