Determine Phase Difference and Time Delay Between Two Pulsed Sinusoidal Signals
Pulse width and frequency alone are insufficient information to determine phase (relative to a fixed point in time or to each other) and delay.  

The main difference between two equal length sinusoids with different starting phases is in the difference between their starting and ending transients.  So after estimating the time difference between the two pulse envelopes, you would have to look at how each pulse envelope starts and ends (which requires having a lot more bandwidth than narrow band frequency estimation alone needs).