The main thing to me looks like the temperature inside the case has risen up.
Since the card (GPU) has it's vent within the case itself, not blowing out the hot air from the back, it's only a half covered card.
What you need to do is remove one of the fans which blow air into the case from the side panel and fix it at the backside of the case to pull hot air out of the case.
That will help reduce temps a bit.
Since you have a new hardware in the rig, the temps are certainly not going to go all the way down to what they were, this card takes power from the PCIe slot, so the temps are going to increase since more power is being drawn from the mobo then was earlier.
And this power to the PCIe slot is controlled by the mobo, so it has to work a little bit more ..... and will dissipate more heat.