If I've understood your question properly, I think this is what you're asking about?
Cyl Bore/Mains/Throws sounds like it refers to the size of various surfaces within the engine.
Cyl bore is how "oversize" (compared to a brand new engine built to spec) the cylinder bore is. On a brand new engine it's 0.000" oversize (hence your 000) As the engine wears, the cylinders start to get fractionally larger (usually in an oval shape IIRC). Eventually, come overhaul time, the cylinder is rebored back to a completely circular shape but slightly oversize. Usually something like +0.020" (020), then +0.040" (040) as a second step. Matching fractionally oversize pistons/piston rings are fitted to ensure a good seal.
Similar principles apply to major bearings within the engine- Mains are the bearings which the crankshaft rotates on, and throws are the bearings by which the connecting rods connect to the crankshaft. Again, these surfaces wear as the engine ages, and again they are machined to remove wear. However, in this case the bearing journals on the crankshaft are machined fractionally (0.020"/0.040") smaller (undersize) to remove any uneven wear, and slightly thicker bearings are fitted (in the case of replaceable shells) or the bearing is relined and ground to the new size.