|You are supposed to NEVER unplug or plug in anything inside the computer case that's connected to the mboard or the power supply while the computer is running.|
Your computer mboard and power supply are probably both ATX - you are supposed to NEVER unplug or plug in anything inside the computer case that's connected to the mboard or the power supply even when the computer is NOT running, unless you unplug the computer or otherwise switch off the AC power to it, because the ATX power supply is always powering the ATX family mboard in some places even when the computer is NOT running, as long as the PS is receiving live AC power.
Did you plug the top drive back in, when the AC power was disconnected to the computer ?
When the AC power is disconnected to the computer, check the data cable connections....
It is common to un-intentionally damage IDE data cables, especially while removing them - the 80 wire ones are more likely to be damaged. What usually happens is the cable is ripped at either edge and the wires there are either damaged or severed, often right at a connector or under it's cable clamp there, where it's hard to see - if a wire is severed but it's ends are touching, the connection is intermittent, rather than being reliable.
Another common thing is for the data cable to be separated from the connector contacts a bit after you have removed a cable - there should be no gap between the data cable and the connector - if there is press the cable against the connector to eliminate the gap.
80 wire data cables are also easily damaged at either edge if the cable is sharply creased at a fold in the cable.
Try another data cable if in doubt.
80 wire data cables must have the proper end connector connected to the mboard IDE header - usually that's blue, but in any case it's the one farther from the middle connector on a 3 connector data cable.
Check your SATA data cables. The connector on each end should "latch" into the socket on the drive and on the mboard, or on the drive controller card - it should not move when you merely brush your hand against it near the socket - if it does, mere vibration can cause a poor connection of it - use another SATA data cable that does "latch", or tape the connector in place.
(There is a slight projection or bump on one side of the outside of the connector that "latches" it into the socket - it's easily broken off or damaged)
The same thing applies for the SATA power connection.
If that doesn't help, you have probably damaged something.
You may have fried the power supply - that's a lot more likely than you damaged the mboard or anything else.
Try connecting a different power supply if you can.