So the trick is to convert your skel mesh to a blueprint (if it is not there already) and make a variable that is exposed to cinematics. Then you can alter this value using sequencer and affect the Niagara system using a Niagara Parameter Collection.
“Test Var” is a variable I made in the skeletal mesh blueprint which is exposed to cinematics. I’m altering that variable in sequencer. I’m then setting “TestFloat” in the Niagara Parameter Collection to a value I set in sequencer and print out the value. This is all you would really need to set in sequencer to drive this FX.
I’ll try and explain this better tomorrow, it’s getting late and I must sleep (3AM here in Florida).