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Fought with clearances most of the day with our LS1. I've been trying to use plastigage, but my clearances all seem to come up too tight. My mains were coming up with .oo1-.0015", and the same on the rods. Stock 2001 block that only had 40,000 on it. stock polished crank, standard King bearings on rods and crank (CR 807HPN- MB5013XP). Eagle h-beam rods. I'm a little lost as to how any of this could be too tight. Questioning the accuracy of Plastgage.
I used plastiguage on the LS2 I just rebuild with all OEM parts. Every bearing (rod and main) was within spec: .0022 IIRC. I think you might have an issue. Sorry...
If not perfectly accurate, it should at least be consistent. I would be concerned about the ones showing .001. Has the main line been honed? If not you're taking a big risk.