How old is the system, in years of use by you.
The bus, or Pci-e graphics slot is governed by the Bios of the motherboard you have.
So taking the card out did ah heck all basically. since it tells the board what it needs and the board says ok here. I have set you up. But the bios of the board is there for example so you can change the link speed of the Pci-e port if it does not get it right, and has to be set up manually by yourself. that is where it is done, most cases it does get it right.
You may of disturbed the card.
And often what happens is people forget to make sure it is set right back in the slot, or or forget if the card requires extra power to run it. And forget to plug them back in. But your case Sounds more like an aging power supply unit as the cause, if it is old, you see they degrade after a lot of running time and become less stable over long term usage.
As a note is the Pci-e bus speed in the bios set to 100Mhz, because if it`s set over that mark then it will also be the cause of crashing so check it`s right in the bios settings since you did a bit of overclocking, it could be the cause without you knowing.
So it is worth taking a look at it as one of the cause for your problems also.
If it is quiet old. Black screen output from the graphics card, and BSOD messages can be linked to it as said though because you took the card out it may also be a case the heat sink and cooler of the card may be the problem by disturbing it GPU over heating so have a check again just in case, as smorizio is saying.
Anyway just a heads up on some of the things to think about as the causes.