Bent rods on a 6NZ....

Working on a 6NZ, blew head gasket on #5, which is the only cylinder that had never been cut and shimmed, even though Cat's overhaul paperwork from 300k ago says they only had to cut 1 counterbore because all 6 had been cut in the past and were 'in spec.' Was not a badly blown gasket yet, had to get it pretty warm before it would blow lots of bubbles. 5 and 6 piston/liners are scored. Anyway, tore down engine, took rods to machine shop to have them checked before using IPD kit, and they say 3 are fine, below what they say the limit of 3 thousandths, one is at 3 thousandths, one is at 10 thousandths, and one is bent 50 thousandths. Has anyone ran into this? Can scoring bend rods like this? Do I have no choice but to yank this entire engine, have the block line bored and put a new crank in it? Is there a chance the crank is fine? No damage to rod bearings, very little wear. Wrist pin bushings still have factory machining marks with hardly any visible wear on them as well. Wouldn't 50 thou damage something??