Determine Phase Difference and Time Delay Between Two Pulsed Sinusoidal Signals I am working on a code that generates two signals: A pulsed sinusoidal signal ($1\textrm{ MHz}$) beginning at $0$ phase, and lasts for say $5\ \mu\text{s}$, then trails zeros. The other signal has the same pulse width and frequency ($5\ \mu\text{s}, 1\textrm{ MHz}$), but begins at a different time ($1\ \mu\text{s}$ later for example), and with a different phase ( $\pi$ radians).  

If either the phase or time delay were consistent between the two, then I would be able to solve this problem, but how do you go about solving this when both variables differ between the signals?  Any feedback on this is greatly appreciated.
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).