The hard drive cable is a recalled part on these machines. You may need to replace it before your drive will be read correctly. The Apple Store will replace your cable for free if it's problematic.
I had the exact same problem. I used Carbon Copy Cloner to copy my old drive to the 1TB Hybrid drive. I put it in and it wouldn't boot. I ended up taking it into the Apple Store and they determined that the cord connecting the drive to the motherboard was faulty. This is a recalled part so they fixed it for free. Once the cable was replaced it started up without a hitch.