Macbook Pro boots successfully when using hard drive in USB enclosure but doesn't boot when connected internally
You have eliminated the possibility of a hardware issue on the hard drive by installing a new hard drive and also by installing the operating system on the previous hard drive via USB.
You have replaced the cable connecting the internal hard drive to the mother board, so it's not a cable problem.
The only thing left seems to be the hard drive controller on the motherboard. I expect the Genius bar will recommend replacing the motherboard.
For an older model Mac like yours, it might be worth searching for a replacement motherboard and having a local Mac repair shop swapping it in for you. It might cost less.