I'm going to go to the store to return it and try to get a 650W because I don't want to risk all the hardwares getting fried.
The opposite will happen! Nothing will get overloaded componant wise except the PSU itself. If it can't power everything, then it gives hardware too little power, and they wont boot - It wont break them though. If the PSU expired in a cloud of smoke, it would (in most cases) just break itself beyond repair.
If you have not taken it back, you dont just want more wattage - A 500W PSU will be fine. You will want one thats of a good quality instead. PSU's from any of these will be a solid choice: Corsair (Their TX or HX Series), Antec, OCZ, Seasonic or Zalman.
For your other question - If you leave the side pannel in place, cooling may be better as you will create a vaccume inside the case. Leaving the pannel at the side wont cause any issues either, but your PC will fill up with dust! If you plan on overclocking that CPU, then using the aftermarket cooler is a must. If you are not into overclocking, then I would personally just use the stock cooler. It will be just as quiet as your aftermarket one
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