Looking good, Tony
I can see a couple of interesting places where the two are slightly different at ~5750 and ~6300. I wonder if the differences are real? There is a telluric O2 band at 6277A but nothing as far as I know at 5750. Christian Buil has an annotated Vega spectrum here which shows the Tellurics.
http://www.astrosurf.com/buil/us/vatlas/vatlas.htm.
If you divide your measured by the filtered library it will show up very clearly any discrepancies. It is particularly worth doing with the reference star itself which should of course match perfectly. You can use any differences to see where you might need retune your response calculation.
Cheers
Robin