You mean .003 - .004? As long as its never been cut before that will be fine. Once you start putting it all back together you can check to see if the pistons are going to hit the heads.
When the motors apart a machine shop will jig it up in either a broach or a mill. Once its centered, level and even to the crank centerline they'll cut it. Just make sure you clean it really good before reassembly.
