Hi!
I'd absolutely start by getting three cans of air, taking it outside, opening it up and blowing it out. Swap out cans as they get cold. You may need to leave the cans in the sun for a bit and start over.
Now we need to try to figure out why it's getting hot. Fire up your activity monitor (Applications -> Utilities) and watch what's going on with your CPU(s). You can click the "%CPU" to sort by what program is loading your computer. Something fun like SETI@home would cause your symptoms nicely.
Another thing you can try is [http://www.bresink.com/osx/TemperatureMonitor.html|watching your temp. sensors]. The program I linked can show you everything that's being monitored by your computer. It might let you pinpoint what's making the heat.
If you think it's the two drives, turn your computer off after it's been on a couple hours, open it up and feel them. If they're too hot to touch, disconnect them and fire it back up for a while. See if the heat problems drop or not. If they're the culprit, get some firewire 800 enclosures for them. Since you're running RAID 1 you probably won't notice the speed hit and your drives will live longer. Yes, OS X will let you raid externals.
Good luck!