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I bought a crank on ebay. It was from an engine that had never been bored. I checked run-out, rod side-to-side play, no up and down play. I replaced outside bearings for good measure, got new seals and assembeld crank cases. After mounting in bike frame, I happened to notice that one side of one rod was pink at the bottom end. Is this bad?  I took pics of both rods. see images

My crank is removed from the engine. I need to tighten the primary gear nut. The service manual sequence to tighten the nut is to place someting soft between the clutch gear and the crank gear and tighten.  I worry about causing damage to the bearings, shafts, gears or cases. Since I have the crank out of the engine, shouldn't I use a clutch holding tool and torque wrench to tighten the primary gear nut, insert the crank and then assemble the engine cases? A different service manual suggests putting the bike in gear and torqueing the nut!