If it's only a small spot the pistons were almost touching without the rock at TDC. When things got warmer I'd expect they got louder... This would be why sometimes simple assmbly isnt the best thing to have done or do. Blueprinting or even more attention to detail during the assembly process would have found that. The harmonics that creates is a mess. If the bearings measure fine (not plastigaged, and not visually inspected) you should probably check all the rods and for straightness and the pistons and pins for deformation too. Pull a couple pin retaining clips and if the piston pins dont slide out with a finger's pressure or gravity alone, you have damage there too.