When i placed the card i noticed that since it is so long it overlaps 2 sata ports, making them unusable, and i'm forced to use the lower row. i have 2 discs, so the long sata cables end up right below the Gpu fan. Is that a problem?
Also, i have a Rosewill fan mounted on the front of my v4, but the board does not have any more 3pins. So i should get a molex to 3 pin or a simple 3 pin to 2x3pin Y-cable?
Finally, since i bought the card used, it has a bit of dust. it idles at 40ºC or so, but still i would want to remove that before it clogs up. So should i get a can of air or use some other method?
40c isn't anything to worry about, especially if your case is as cluttered as your sounds. And to get the case fan going I'd just use a molex to 3 pin adapter on the quietest fan you have, plug in the rest.
As for cleaning the GPU I'd pull it out of the case and use compressed air on it, making sure to hold the fan(s) still so they don't spin. The reason you want to take it out is because you want to keep the can of air vertical to avoid any liquid while hitting the fan from different angles.
You can remove the GPU to clean it or if you lazy and doing regular cleaning of it do what I do, turn off the computer and with it off blow the compressed air in the fan intake and than the exhaust and repeat as neccessary to knocked loose and out all the dust. Just keep remember to move the attached straw which most come with to get into those hard to reach places while keeping the can vertical.
But a 40c idle I am not worried about as trapper mentioned, what really matters is what the temp at load. But so far it sounds like your case is mostly clean and free from obstructions so I wouldn't worry too much about that.