I suspect you have too many zeros and it's actually .006". Thats pretty close to average on the late models I see here in the shop. At the stage 3 level, you are increasing power substantially and adding more stress to the crank substantially. If you have not already paid for all these parts for the stage 3 I would very strongly consider going with an S&S crate 124. They're damn near bulletproof out of the box, run quieter, make great, real world, useful power that can be increased even further if you want more later on, they're available in granite CVO color now and they damn near pay for themselves in the cost savings you have in labor over building a motor that is going to put out the power in the same ballpark as the S&S and to add a little more icing to the cake, they have a warranty that they actually stand behind! All you have left to address is the throttle body, injectors, tuner and a clutch and you're there! And as required to be a vendor here, Id be more than happy to set you up with everything and a great discount. Yo add to that, you can sell your heads cams and some of the other stuff that are still desirable for other guys doing builds to help fund the whole thing.
Edit: If you decide to build what youve got, I would either get a set of S&S flywheels and replace yours with the increase in power you intend to make or send your to Darkhorse to be reworked. You didnt say if this is an A or B motor. If its a B without question I would do something to the bottom end. The interference (press fit) sprocket on the crank to drive the cain to run the counter balancers are weak. They will move if you put the power to them them and your motor will be out of balance. The factory setup has no splines, no woodruff key, no flat slide, nothing to help keep it from spinning out of time. Big POS.