what have I done to my mega2560???

So was going great guns last night after work, and decided it was time to up the ante.
I want my usb bought on my Arduino 2560 to be a usb midi port, so I will flash the u8. Then to program it I will use my AVR ISIP mkII. and power it from an external power supply.
Firstly, is that a bad move - to have the usb connected and an external power supply? If I convert the u8 chip to midi will it still power the arduino?

Secondly, and the real question. I plugged the external power supply in and realised it was center negative/positive - whichever way round is the wrong was around for arduino. I swapped it around and the power light came on, and the led 13 came on. When I hit the reset button, the led 13 goes out then comes back on again. This tells me (I think) that the bootloader is still present?
When I look in device manager I see arduino on com 34. However in arduino IDE it does not appear under as a serial port. When I try to program it using avr isp mk II, it get AVR Dude complaining that it couldn't find USB 'usb'.

So the question is have I fried something? Can i resurrect it? Should I start by trying to burn the bootloader in AVR Studio? Is there any confirmation as to whether anything is bust?
Cheers guys

I see arduino on com 34.

If you are using windows, can you go to device manager and change it to a com less than 10? That might help.

Yeah, I'll do that when Im back from work, just seems a little too much to be a coiincidence that when this all happened I cant connect.
Does the fact that it appears in the device manager give you/me hope that I might not have fried something? (he says hopefully...)

See this discussion about using USB and External Power at the same time:
http://arduino.cc/forum/index.php/topic,82046.0.html

Does the fact that it appears in the device manager give you/me hope that I might not have fried something?

That tells you that the USB to serial chip is probably working.

So I've bricked the usb port. When I get home I will try once to flash the atmega8u2 with the firmware again, and then write to it. Otherwise I can try I suppose to program it with my isp mk ii and then with my serial to usb cable get info back to the terminal for current development but eventually I will need usb back...
I wasnt quite sure though from reading that thread - if it appears as Arduino in device manager does that tell us anything?

Saved it!
Using avr studio I re burnt the firmware to the mega8u and everything works perfectly!