You might be reading some of the chamfer.
I've heard of peoples methods of removing error like putting a piece of paper in the port till it touches. The best method I've heard is taking two wheel readings with a 0.020" and a 0.010" feeler gauge in the port; then the real opening is the 0.010" reading minus the difference between the two.
So, I think you might need to add a bit more exhaust duration and try to flatten the entrance of at least the exhaust side transfers.
Also, you may want to unshroud the lowers. Mark the piston at BDC and then match the lowers to the piston shape.