I afraid you might be in for a struggle having done this upgrade on a mid-2009 15" MacBook Pro and I'm not alone in having the problem. I ended up having to replace the drive cable and switch to using an SATA2 rather than SATA3 drive to get an replacement drive (SSD or magnetic) to work. The problem is documented on the OWC web site.
As I recall, I got a larger replacement magnetic drive to work by downgrading the firmware but getting an SSD to work required upgrading to firmware, replacing the cable, and getting an SATA2 drive. If you already have the drive, start with the cable and maybe that will be good enough.
I've cloned lots of drives to external drives and then swapped in the external drive for the internal without a problem so I think it's far more likely you have the hardware compatibility problem than a software issue.
BTW, even with a SATA2 drive, the upgraded system flies.