MAC OS now reinstalled on internal drive but MAC will not boot from it

A MAC Pro was booting up and getting a flashing question mark folder.

According to many online pages, I decided to make a 64GB USB stick into my bootable disk for the MAC. I created this with transmac I installled the MAC OS Lion .dmg file on it.

Despite all instructions, I just could not use disk utilities to use that USB stick to reload MAC OS Lion onto the internal drive.

In the end, I removed the internal drive placed it into a USB Chassis, cleaned it plugged it into the MAC Pro USB port. So I had the USB stick with the .dmg loaded on it in one USB port and the original HDD plugged into another USB port, in an external chassis

In the end I managed to reinstall MAC OS LION on the HDD that was in the external chassis and the MAC book pro now works but is booting from its original internal disk but that disk is now in an external chassis. It's now in effect an external drive that boots the system up and it runs

So I stupidly assumed I could then just take that HDD and install it back inside the MAC and reboot the MAC. I assumed it would boot then from the HDD now all reinstalled with MAC OS Lion but now back in place inside. Meaning no devices now plugged into any USB ports

It does not now boot and will not boot from its internal drive. I was trying to find a way of making the MAC look for its HDD first and boot. Tried many ways to make it boot from the internal HDD. To no avail.

How can I make this now boot from this internal HDD which I know has the OS on it and works if its in an external chassis....I do hope somebody has the answer.