Mine is almost as bad I guess - difficult to compare really.
Overclocking shouldn't really harm the PCIe port on your pc. The GPU could, in theory, be damaged by overclocking and overvolting, but the actual port is mainly a passive bus and shouldn't be damaged. One thing I have seen a lot of lately though is bad capacitors around the PCIe connector. You can check them visually (do a search on youtube for "motherboard capacitors" and watch a couple of videos), but I think the behaviour of your card is pretty normal. The GPU and memory on your card will go into power-saving mode as soon as you stop any intensive activity (like switching from a game to desktop). In this mode the clock speed of both is lowered, but there is usually sufficient power to run the windows desktop. You could try using a third-party utility to stop the power saving mode which should have an effect on the window lag, but tbh low-power mode extends the life of your gfx card and other components in your pc by keeping it considerably cooler when idle.