The .010" lash will change the valve lift by the lash x the rocker ratio. So you should be adding .016" to the measured lift in your computations.
Just to check the geometry correction: Look at roller position on the tip of the valve right at exactly mid-lift point. If the geometry is as good as it can be, then the roller will have moved as far out on the valve tip right at mid lift, and will roll back in across the tips about equal amounts at both at full open and full closed. It may not be exactly this but should be close.
I can't see .040" short on valve lift being just from the pushrod angle. The 'cos 11* x .409" tappet lift' works out to .4014" and multiplied times 1.6 is a loss of .012" at the valve. So there is more going on. Know that, even with geometry correction, there will be some loss in lift due to the rocker rotating through a very wide angle; your lifts are getting so high for the rocker length that it is reaching the point where the unusually large rotation angle starts to result in significant loss of vertical motion.
