Exactly..... that is why I doubt the effort to set valve stem heights to the existing spring seats is gonna fix anything.....and may make things worse. There is NO way to know if the seats are all anywhere near to being at an even height to start with. And determining valve height by looking at lash is looking at things the wrong way; the stack-up of parts tolerances in the valvetrain makes lash a 100% unreliable way to set valve stems heights.
Understood on the cost factor.... Changing the rockers around and having preloads change is no surprise; they are just stamped pieces of metal and only have so much accuracy in their dimensions.
Is it possible that when you think you are at #7 TDC you are actually at #4 TDC? Remember, #7 TDC on the chart you are using means that the #4 valves are at overlap (both #4 valves slightly open).