Failing to Upload Firmware for APM 2.6

NMAIST

Beginner.
Hello All,

After trying to update some custom code onto our APM in order to add some sensors to our copter, we ran into a few roadblocks. Our code was not able to upload due to some error and we also figured that our attempt to upload code had messed with the firmware we had previously installed. We have been trying to re-upload our old firmware(using mission planner) but have so far been unsuccessful.

The first time we tried to re-instal the firmware, we got a message that said:
"System. Exception: Upload failed. Lost sync. Try Arduino!! @ Mission Planner. Utilities .Firmware.Upload Flasah (string comport. String filename,boards board)in C:\Users\hog\Documents\Visual Studio 2010\Projects\Ardupilot Mega\Ardupilot\Mega\Utilites\Firmware cs:line 1066"

Second try onwards, we have been getting the following error message after getting 75% through reading the hex file:
"Check port setting or Port in use? System.10.10Exception. A device attached to the system is not functioning"

On APM Planner we got :" Unable to open COM port: usbmodem1421"(we tried using the other USB port on the laptop and got the same error.

The board does come up in the device manager under "ports" but we can't connect to the board at all. We read online that some people used APM Planner and that seemed to solve their problem, and tried to use APM Planner which didn't work either. Flashing the bootloader is not really an option for us because we don't have an Arduino Mega(which a lot of people seemed to say was necessary to flash bootloader). The APM board lights up as usual when we connect it to our computer(Flashing green ad orange lights) and the blue light flashing slower.

Sorry for the extremely long explanation but we really need to get the copter working again and any help will be much appreciated.

Thanks in advance.
 
Update: Now, every time we try to go to the "Initial Setup" tab and choose "Install Firmware", we get an error:

"There was an unexpected error".
 
Also, how can we possibly check what firmware we have and what is the latest firmware version for APM 2.6?
 
It's connecting to COM3 (via USB) and COM4 (via telemetry). We have checked and there are no excess COM ports in the "Ports" section of device manager. We are using Windows 7 and we have also used Mac Os(Mavericks). We are not sure exactly what bootloader we would use. We found instructions for a few, but we can only use bootloaders that can be executed using an Arduino Uno. Any specific examples and links on that would also be useful.

Update: We have still not been able to load the firmware onto our APM 2.6. We are not even able to start uploading firmware because every time we go to the "Install Firmware" tab, we get an error message: "There has been an unexpected error".
 
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