Power Supply Upgrade Fallout

So I attempted to upgrade my power supply, from a Coolermaster atx12v 650 to a Thermaltake tr2-600nl2nc atx12v and found the new power supply defective after hooking it up and finding it unable to power my computer properly, lacking 6 of the requisite 24 pins necessary to connect to the motherboard properly upon close inspection, though not the wires, which is why I hooked it up in the first place.

However, now that the devil has been disposed of, the ghost still seems to remain in the machine. My restored power supply is very clearly powering all of the components of the computer, from hard drive, to fans to dvd, blue ray, hd, and all my other sundry drives. It is even providing power to my externals, though not all of them, as my mouse lights up, but not my keyboard. But something is not happening. The monitor is detecting the graphics card when power is in the computer, it makes a distinction between no connection and a connection when there is no power present. But no matter how I arrange the wiring, no matter how I test it, the computer acts as though it is booting, then behaves as though it has, but the speakers, monitor, and keyboard are quite insistent that it has not. Anyone know what I did to my computer?

 

What i would probably do in this situation is disconnect every thing even the coms battery on the mother board let it sit for about 5 to 10 mins and reset it self.

Then plug in every thing one at a time.It might be a pain in the but it is all ways good to eliminate each items that could be causing the issue.