54 celsius is 129 degrees fahrenheit, which is well within specifications for your CPU, though a bit higher than ideal. 90c is definitly way high, thats 194f, above failure point.
If your CPU fan is working correctly, you shouldn't be able to get anywhere near that temperature. your computer would go into automatic thermal protection mode and shut off (which is a feature of the motherboard you have). THe stock CPU cooler with that CPU is fine. A better cooler will help, but you shouldn't need one in the first place. Water cooling would certanly also help, but you don't need it for the level of components you are running. Plus then there are a host of other issues that go with it. I run water cooling setups on all my computers except the mill controller, but air is definitly easier to install and set up. For water cooling you have to remember to top off the coolant every year, you have to disable the CPU fan sensor in bios or else press F1 at every startup for the rest of your computers existance, and you have to make sure your computer is never stored at below freezing temperatures. Its definitly doable though, and thats not a bad starter kit.
Case fans, a pair of 120M or larger fans should be fine for most situations. Adding a third fan to a gaming computer, especially if you have a mounting hole for it would not be a bad idea. You can also make your own hole and mount one easy enough.
I'd be inclined to suspect first that you might be getting a faulty temperature reading. Where are you getting that number? To get the actual motherhboard sensor numbers, go into Bios at computer power on, and down to the hardware monitoring tab.
If those numbers show high temperatures at idle, then you have a hardware problem. Chances are, the heatsync is not properly installed, or has came loose. Those plastic pins they use the stock heatsync can sometimes fail, causing a corner to lift. In that situation though, the computer should instantly detect a heat spike and shut the computer down. Given history with that particular motherboard, i'm hesitant to reccommend reseaing the fan, but with the machine off, you may want to reach in and see if the fan base wobbles or is loose at all. Also see if any wires might be slowing the fan down or impacting it.
If you want to eliminate the stock fan as a suspect, and especially get rid of those evil pins, you could upgrade the cooler to a better air cooler if you don't want to spring for the water cooling setup. This one ($45) is fairly easy to install: http://www.tigerdirect.com/applications/SearchTools/item-details.asp?EdpNo=6085172&CatId=798
To put any of the aftermarket coolers in, you will most likely have to unscrew the motherboard to install the backplate. Once you have that in though, the replacement cooler basically just screws in, which leaves much less to chance. The water cooling unit is a better cooling solution in the long run, but either one should be fine for what you have in the case.
If the fans are all working and the CPU fan isn't lose, it may be improperly applied heat sync grease. Either too thick, not thick enough, or containing air bubbles. Or possibly a bad batch of artic silver. If you ever had to pull the CPU out and replaced it without wipeing off the old grease and applying new, you might have small air bubbles, which can cause excessive heat.
Another thing that could be contributing, is fan airflow. The front case fan should be bringing cooler air into the case, the rear fan should be exhausting it. On a computer fan, the bracket portion of the frame that actually holds the spinning part of the fan should be towards the rear. Air exhausts over the four arms of that bracket. On the front fan, you want that bracket pointed towards the inside of the case. On the rear fan you want the bracket up against the back wall.
If either of the fans is pointed the wrong way, you can create an overpressure or underpressure situation, and dramatically reduce air exchange. Cases also need a minimum of 1 inch, prefferably more around any exhaust vents for proper air mix. If you are venting hot air too close to a wall, it ends up cycling inside the case and bakeing things.
Is there any chance that CPU temperature was actually the GPU? Graphics cards run hotter than CPU's by design. 90 is still high, but i'd feel better about that being the high temperature than your CPU.
Another thing to try if feasable, is run the computer with the side panel open. If the temperature immidiatly drops, then you have an airflow issue inside the case. if it doesn't drop appriciably , it may be the CPU heatsync or a sensor error.
If all that doesn't do the trick, it could be a sensor glitch. Asus motherboards sometimes have sensors that are off by 10-15 degrees from the factory due to bios issues. They usually fix that in a bios update. Updating the bios on an asus motherboard is actually a pretty easy process. You download the bios for your motherboard from support.asus.com, unzip the file to your hard drive, then restart into bios and run the built in Asus EZ flash utility. If it doesn't like the bios file or it is corrupt for some reason, it won't flash. If the power dies during flash, it will revert back to the old bios. The only downside to updating the bios is that it will reset your bios settings. the biggest potential impact there being that you may have to reset your boot device order or any other custimizations you may have made.
Try those things, and if that doesn't do the trick, let me know and there may be a few other things we can try.