Fast modulation based on analog signal
Firstly you will absolutely need an AOM operating in the VHF region, the common 27MHz sort used for Q switching or in old laser printers will be unlikely to cut it, they have rise and fall times too! 

I would finesse this in something like the following way if doing the FPGA thing: 

U1 and U2 come into the FPGA digitally, and are converted to a single (or at most a very few) bits of SDM output at maybe 100MHz or so (FPGA digital doings have no issues with that sort of speed), a toy little lowpass network produces an analog signal with a 1MHz or so bandwidth and a swing of about 1V or so for each of U1 and U2, then use two of the LVDS inputs as comparators (They are fast) to do the windowing thing. 

An alternative is to feed U1 and U2 to a DAC (Fast DACs are more common then fast ADCs) and then do the windowing thing either with some fast comparators or again with a couple of LVDS inputs to a small FPGA (Means you can do neat things like programmable delays and pulse stretching fairly easily).

On the output, buffer then drive the input to a diode ring mixer or PIN diode switch to control the AOM RF. 

The quick way to build this is with comparators and have them switch currents into a diode ring mixer or PIN switching diode, you probably want to be doing physics, not mucking about with logic.