Unfortunately the Arduino IDE can't use the AVRISP MkII using the standard USB drivers so I had find some other way of burning the bootloader.
I don't understand that. Isn't the AVRISP Mkll driver already installed when you set it up to function with AVR studio? Once the driver is installed it's the PC that senses when you plug in the programmer and uses the preinstalled driver. The IDE does have a AVRISP Mkll choice in the bootloader programmer selection menu, so as long as the programmer is already plugged into the PC, then choosing that programmer should work. That's how it works for my USBtiny programmer, the driver didn't come with the IDE disturbution nor did it install it, that was done prior when the PC first saw the USBtiny was plugged into the PC and asked for a driver source.
Anyway your statement has me confused, could you explain further?
Lefty