OK, why is the bluetooth working on COM5? Is that your PC's bluetooth? If so, then ignore it for now. You only want the COM3 port talking to the UNO for starters and sketching.
Check these threads for samples: http://arduino.cc/forum/index.php/topic,120113.30.html and http://arduino.cc/forum/index.php/topic,105045.0.html We've been working on a few things with the bluetooth. Keep in mind that what we are working with is the Seeeduino Bluetooth Shield so your code for the void setupBlueToothConnection() is going to be different. You should be able to use any pins on the UNO (except pins D0 and D1 as these are used for the communications between the PC and the UNO). The "Wiring Example" given in the Sparkfun sample is very specific to the board that they were using. Also read this Arduino Playground - Tutorial01 it's the same as the Sparkfun info but has more details.
Remember, you have to setup the bluetooth module first and then get it to pair with the other bluetooth device before they'll start talking back and forth. The setup is usually easy but the pairing has been a bitch for some of us.
Make sure you read and read again the info given for you particular bluetooth module that you're connecting to the UNO.
This: http://www.sparkfun.com/datasheets/RF/BlueSMiRF_v1.pdf and this: http://www.sparkfun.com/datasheets/Wireless/Bluetooth/rn-bluetooth-um.pdf for some of the commands needed to setup the BT module. It's gonna be kind of hard to visualize all of the communications that are going to be taking place to get things working. Communication between the PC and UNO; the UNO and the BT module; and the BT module and what ever other Bluetooth device (whether the PC's BT or a smartphone/tablet)(I'd recommend a smartphone/tablet so there won't be any conflicts on the PC).
Good Luck... and remember, We're all counting on you.