You need to measure the bearings with a caliper. Then you measure the bores without the bearings in it. Do the math between that and the crank's main journals and you'll have your clearance.
You could also measure with the bearings in but you have to check inside and outside of the oil groove. Takes a steady hand but it's doable.
If you're measuring 0.0002" off on the bore, that's nothing man. You also measured with no head bolted on too! Easily the deck under load will distort the cylinder walls up to 0.0004".
You measure the bores by bolting the head back on with your old head gasket (clean it up), flip the block over and measure the bores that way.
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