to the story on the piston going through the hood.... not sure how the piston came through the head first...?????
One thing that hasn't been discussed is bearing clearances... USE the FSM, it is your friend. I typically use the middle of the spec for main bearings (+ or - .0005"). When it comes to rod bearings I usually run clearances just loose of the middle of the spec.
Use new rod bolts(came with rods) Check with Eagle for their torque spec for those rods.