iMac only boots into Safe Mode after GPU replacement

Can you boot into the Recovery HD? Have you checked that nothing is affecting the SHIFT keys?

Try:

Reinstalling Lion – Yosemite Without Erasing the Drive

Make sure you have a current backup before proceeding.

Boot to the Recovery HD: Restart the computer and after the chime press and hold down the COMMAND and R keys until the menu screen appears.

Repair the Hard Drive and Permissions: Upon startup select Disk Utility from the main menu. Repair the Hard Drive and Permissions as follows.

When the recovery menu appears select Disk Utility and press the Continue button. After Disk Utility loads select the indented Macintosh HD entry from the the left side list. Click on the First Aid tab, then click on the Repair Disk button. If Disk Utility reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported click on the Repair Permissions button. Wait until the operation completes, then quit Disk Utility and return to the main menu.

Reinstall OS X: Select Reinstall OS X and click on the Continue button.

Note: You will need an active Internet connection. I suggest using Ethernet if possible because it is three times faster than wireless and more reliable.

I think you may have a bad drive or other hardware failure. If you have an external drive that has a bootable system on it, then see if you can boot from it. If you can, then the internal drive is toast.

If nothing changes then you have a hardware issue on the motherboard.