I was concerned that what I thought was fractional frequency deviation might be different from clock peoples definitions of fractional frequency stability. I looked around a bit and here is what I found out:

References:

• Characterization of Frequency Stability
  
  • This is the Bureau of standards note debating what standard to use for Freq. Stablity. It  discusses Allan Deviation versus Spectral Noise Density, and their relationship
• The Science of Timekeeping
  
  • AN HP note explaining the relationship between Allan Deviation and Spectral Density - see page 63 for general integral relation between the two quantities
• A Frequency-Domain view of Time-Domain Characterization of Clocks and Time and Frequency Distribution Systems
  • David Allan document explaining the relation between Allan Dev and Spectral Density - He doesn't give the exact form of the transfer function you should apply to get Allan Variance from a PSD, but he shows plots of it which are consistent with the previous analytic form.

I used this to make some plots of the Allan Deviation from my power spectra, the units of Allan Deviation are dimensionless, as its a measure of fractional instability.

I found a typo in the old code, uploaded new plot.

Line / X's are calculated from the PSDs.

Circles are directly calculated Allan Deviations.

Moral: LOOKS GOOD!