If I'm remembering correctly, you shouldn't be able to put the shafts on the wrong way due to the the holes needing to be down and the oil holes will be exposed away from the rocker if you put the shaft on backwards
I'm not sure about swapping sides making the shafts different
I do know that some of the middle rocker shaft hold downs don't have oil holes in them so they need to be installed correctly on both heads to oil the rocker arms