Without any PC information nor detailed overheating problem that only thing that I can say from your post is if only one GPU fan is working out of 2 or 3 (depending on your GPU model) that would cause your GPU to overheat since it needs both fans running at full speed to keep the GPU from overheating.
Also when your replaced the Thermal Paste and Pads you could have incorrectly applied them or your may have damaged the wiring to the GPU fans or one of the fans itself during your maintenance.
Most likely you probably voided your GPU Warranty by replacing the Pads or taking apart the GPU card. That will depend on your GPU Manufacturer's Warranty.