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Thinking about it, the MT6 Maguras I have had a similar problem.
The solution I found was use the standard bleed block and do a bleed, except when the bleed is good, remove the bleed block, mount the caliper on the bike with pads, pop the wheel in, then open the caliper port and push an additional amount of fluid in to close the gap between pad and rotor, close the port, remove the wheel and pads then tidy up.
Anyone tried using undersized bleed blocks or DIY bleed blocks to bring Shimano road discs free-stroke / lever-throw down?
https://www.shapeways.com/product/A9DAXVXWP/bleed-block-5mm?li=shareProduct
https://www.shapeways.com/product/NN5BKSGNJ/bleed-block-1mm?optionId=57888666&li=related-items
from: http://forums.roadbikereview.com/components-wrenching/shimano-r785-disc-levers-have-excessive-free-stroke-343759.html
With the pads a bit worn my levers are almost bottoming out. If I remove the wheel and squeeze them they reset to be too close so the brakes are 'on'. It's getting a bit annoying.