HDD won't boot fully.

I couldn't boot up my HDD on to my other MacBook pro, as it refused to unmounts after trying everything, plus sudo codes. Anyway I wiped it on another mac with an external hdd cable, got a bootable Yosemite usb done. However it would not set up OSX when my HDD was in my mac. So I then took hdd back out and tried to set it up external and Bingo it worked got a full working mac. However I cant transfer this hard drive back to my mac, as it only boots half way, I know I have done something wrong. Any ideas? The cursor line under the apple will only run up to the half way mark, and does not seem to be moving. I have plenty backups on another external HDD from time machine. I am wondering what to do now. I can work it with the external adapter, but I want the drive in the machine.

Regards