..How critical is it that the stock rods and pistons be installed in the same cylinder they were removed from? Say for example in a 5.3 iron block. Talking about where the rod meets the crank.

 

It's not. If you had aftermarket pistons and the block was machined to "fit" each piston to it's bore it would be different, but the factory doesn't take assembly to that level. If it's within tolerance it's fine. Piston to wall clearance should be 0.0007" minimum to 0.00212" maximum.