As far as I'm aware there are no disadvantages to using case fans (or stock fans as you call them) although you may want to buy a few in order to see noticeable changes in temperature. What you should be on the look out for is an after market heat sink fan (the fan which attaches directly to your CPU). The Cooler Master Hyper 212 Evo is a very cheap and good heat sink fan available for purchase.
Besides, your temperatures don't strike me as really high temperatures. Some rigs can get up to 70 degrees C on full load and they will be fine.
Thank you for your help. But one last question: so you don't think that the graphics card is to hot and you think that the processor is hot?