Case/GPU swap, couple of issues

[dull merlin]

Mobo: Z590-A Pro
CPU: i5 10400
GPU: 4060ti
RAM: Vengeance 16gb DDR4 (x2)
PSU: CX750M
Storage: Samsung 870 EVO
Cooler: h100
Case: 4000D

So I recently bought a new case and GPU and did a case swap. Upon removing the old 980 in the lower PCIE slot, the PCIE lock was stuck which required more wiggling and pulling than I felt comfortable with. I installed my 4060ti in the same slot, put my covers on, and the PC booted. Not long after, my keyboard, headphones, and/or mouse would disconnect altogether. I have since flash updated the bios, downloaded all drivers from MSI's website, done a windows update, and ran into the same issue. Frustrated and concerned it was something to do with hardware, I stopped using it for a few days and returned to different forums to troubleshoot. I have since replaced the battery on my motherboard and switched my GPU to the top PCIE slot. I think I may have damaged some pins when removing the old GPU. My USB devices are no longer disconnecting since, but I feel like it's taking longer to load things and that my PC is running slower in general. The RGB on my keyboard is stuttering/losing frames while in game. I also noticed a quick "flash" on my screen, almost like a blink or "flicker". I'll include a picture of it.

Besides those symptoms, I've been monitoring my temp's in iCUE dashboard and everything is running at normal temps while idle/under load. I'm getting 30-40 celsius while idle and between 50-60 while gaming. I have a family friend who does IT and such that is willing to take a look at my PC in the near future, but until then I figured any help here is appreciated. Thanks.

[storm whale]

the issue might just be a bad display cable with the gpu installed in the top slot that you didnt notice before on the older gpu, specially if you were not using the same type of cable, like switching from hdmi to displayport

never force your gpu in or out of the slot. the lock requires a screwdriver or preferably something less sharp to push it open if it's tightly locked

why were you using the lower x16 slot for your gpu when that one is only wired for x4 pcie lanes instead of x16 on the top slot? that second x16 slot only supports pcie 3.0 bandwidth, so your 4060 ti would run even slower in that x4 slot.

[solid zodiac]

Did you run DDU to uninstall the old gpu drivers and install the updated fresh Nvidia drivers? Also, iCue has a tendency to cause weird issues too. You might try updating it or uninstalling and installing the most up to date version of iCue.

[storm whale]

gtx 980 and rtx 4060 ti use the same driver package, assuming they were using the newest or newer versions

the issue looks more hardware related than driver

especially with disconnecting and reconnecting usb before swapping pcie slots