I went through this same process this last spring. What I found, for me, is that all this book theoretical data is enjoyable to read...but left me overthinking the process. Light transmission, clarity, parallax, bullet compensation, etc...
The one overriding thing that made me decide upon my 40mm instead of a 50mm was Fit...Cheek weld and eye relief. Two things that are not often discussed when speaking of the technical merits of a scope.
Now that I am getting into MOA adjustments, instead of windage holdover, My perfect scope would be a Swarovski, fine crosshair, 40mm. Recticle is in the first optical plane, means that rectile placement on the target does not change with different power settings. It is really good glass. Fine crosshairs do not mask as much of the target at longer distances.
For a field report: I did side by side comparison between a Leupold VX-II 50mm and my VX-III 40mm after sunset. Astounding, my VX-III 40mm was more clear, brighter and showed better color than the 50mm....I did not have my light meter with me, but It seemed 30% better on all counts to me - and my friends.
I think glass quality is paramount. No book I ever read said that a 40mm could out perform a 50mm.
Get the best quality glass you can afford, and make sure of the fit.
Perhaps a local shop would let you place a few 40s and 50s on your rifle and see what fits you best.