did u have the mains checked on the block and then checked the crank to see what they were? I would run .0028-.0035 on clearance. Make sure the rods are good to for clearance.
Ryan at Shady Dell is porting my heads and sold me the scat crank and rods, and balanced them. He measured and ordered me proper rod bearings. Its up to me to check main journals and thrust. Of course I'll double check rod clearance and side play when I put it together but so far I only measured the mains. Thrust was right on @ .005 but the bearings are all .0016-.0021 too tight if I'm going for .0025-.0030 clearance.
I never align honed this block but it lived for seven hard years with an eagle 4" crank and standard bearings redlining at 6k and running around 410hp