Trace A is what you are getting with your Flip-flop.
Trace B is what you would settle for (1uS low pulse).
Trace C is your ideal. The resulting bit pattern is along the bottom.
Trace C is probably not practical. Your low period should always be shorter than the 2uS bit cell period. So a duration of around 1-1.5uS should do.
We'll use a monostable to generate the low pulse, triggered of the falling edge of your waveform.
Could have used the 74121, but we need it to be negative edge triggered and the '121' only has a Schmitt action on the positive going B input. The above will probably work, at least for experimentation purposes, but not sure how stable the output duration will be with temperature and supply voltage changes.
Circuit A uses a Schmitt action input. Circuit B will be more prone to any noise on the input signal, but should probably still work satisfactorily.