Blown USB controller and Uploading sketch through ICSP header

I am currently in the process of building a RepRap Prusa Mendel Iteration 2 printer. With this printer I have acquired a RAMPS 1.4 card and all the items that come with it.

After plugging in a thermistor without turning off the main powersupply of the RAMPS, the Arduino Mega 2560 is no longer recognised by the computer. I have tried with a couple of computers, none see the Mega.

My fear here is that I have been able to blow the USB controller, possibly also the voltage regulator, though it still seems to take 12V in and the LCD is only a bit dimmer.

So my question is: Can I uploade a new sketch to the Mega without using the USB port? If so, how?

I have tried going through the ICSP headers, though I do not have an external programmer, so I use an Arduino Uno with the ArduinoISP sketch uploaded to it and "Arduino as ISP" selection selected as programmer. My wiring is as follows (UNO:ICSP header Mega) 12:1 5V:2 13:3 11:4 10:5 GND:6

I have tried to reupload the bootloader, both to the main ATmega 2560 chip and the ATmega16u2 chip with this method, and it seems to work. When it says the bootloader is done uploading, the Mega seems to have the standard Blink sketch uploaded. My problems again seem to arise when I try to upload another sketch through the ICSP headers. Symptoms: When the bootloader has been newly uploaded, the onboard LED blinks with about 1 second delay between on and off. When I try to upload another sketch using "Upload using Programmer" with "Arduino as ISP" set as the programmer, the TX and RX LEDs on the programmer UNO blink. I get no errors and a message "Done Uploading" The Mega board now continously lights up the onboard LED, this happens no matter what the sketch I try to upload is.

Summary (TL;DR): Uploading bootloader seems to work Uploading other sketches does not work How to upload without using USB connector?

Plugging up the Uno to the Mega through the digital pins as opposed to through the ICSP pins I at least get the message "Done uploading."

My wiring is now as follows: 10:Reset 11:51 12:50 13:52 5V:5V GND:GND

Connecting the RAMPS board leaves me with the same result, however.