Why can I only boot my computer with my Windows 7 Ultimate DVD

I currently removed my motherboard and all of my components to install a new heatsink/fan. After I put everything back together, I get a MBR or some error stating that the computer won't start. After rearranging some cables the computer booted and never went past this black screen and a blinking cursor. I used my Windows disc to repair my computer and nothing. I used the command prompt with some help using the command line bootrec /fixboot. There was also instructions to use command line bootrec /fixmbr which I didnt perform. I know what MBR stands for so maybe I should have tried that, but I didnt. After I completed the command I mentioned, the status light stay orange and the computer hanged. I used Windows disc and it asked me to boot from DVD and I let that message pass and then the computer boots. I always have to use my disc to boot Windows.