Bad machine work or am i over looking something?

You may want to see if those two studs are bent... If they are cocking the thrust they will try to **** the next cap you use them on and at minimum affect the oil clearance. I've seen them get bent at a shop when the block was lifted using a strap and overhead hoist into a peice of equipment. The #1 cap was not torqued and the leverage was enough to bend the studs. It was noted when they did torque the cap and it wouldn't line up. In any case - as was noted by CP - the studs need to be fit to the caps - somethings they holes need enlarging - then the caps torqued a couple times, then it should be line bored and honed.