Hiho,
i got a few steps further

still when i try to upload the bootloader to the atmega2560 using ArduinoISP i get:
avrdude: verifying ...
avrdude: verification error, first mismatch at byte 0x1e000
0xff != 0x0d
avrdude: verification error; content mismatch using:
Commands used:
avrdude -C/Applications/Arduino.app/Contents/Resources/Java/hardware/tools/avr/etc/avrdude.conf -v -v -v -v -patmega2560 -cstk500v1 -P/dev/cu.usbmodemfd141 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0xFD:m -Uhfuse:w:0xD8:m -Ulfuse:w:0xFF:m
avrdude -C/Applications/Arduino.app/Contents/Resources/Java/hardware/tools/avr/etc/avrdude.conf -v -v -v -v -patmega2560 -cstk500v1 -P/dev/cu.usbmodemfd141 -b19200 -Uflash:w:/Applications/Arduino.app/Contents/Resources/Java/hardware/arduino/bootloaders/stk500v2/stk500boot_v2_mega2560.hex:i -Ulock:w:0x0F:m
Anyway i finally figured out that i need to use the second icsp header to access the 8u2/16u2 interface

so:
avrdude -C/Applications/Arduino.app/Contents/Resources/Java/hardware/tools/avr/etc/avrdude.conf -v -v -v -v -pm8u2 -cstk500v1 -P/dev/tty.usbmodemfd141 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0xFD:m -Uhfuse:w:0xD8:m -Ulfuse:w:0xFF:m
avrdude -C/Applications/Arduino.app/Contents/Resources/Java/hardware/tools/avr/etc/avrdude.conf -v -v -v -v -pm8u2 -cstk500v1 -P/dev/tty.usbmodemfd141 -b19200 -Uflash:w:/Applications/Arduino.app/Contents/Resources/Java/hardware/arduino/firmwares/atmegaxxu2/MEGA-dfu_and_usbserial_combined.hex:i -Ulock:w:0x0F:m
seems to work fine (no errors)
but still i get:
[0xffffff804b1eee00] The IOUSBFamily gave up enumerating a USB device after 10 retries. (Port 4 of Hub at 0xfd100000)
when i plug the fried Mega to usb.
I then found the Atmega_Board_Detector from Nick.
reading the ATmega8U2 ICSP gives me:
Atmega chip detector.
Entered programming mode OK.
Signature = 1E 93 89
Processor = ATmega8U2
Flash memory size = 8192
LFuse = FF
HFuse = D8
EFuse = FD
Lock byte = CF
Clock calibration = 5D
Bootloader in use: Yes
EEPROM preserved through erase: No
Watchdog timer always on: No
Bootloader is 4096 bytes starting at 1000
and reading the ATmega2560 ICSP gives me:
Atmega chip detector.
Entered programming mode OK.
Signature = 1E 98 01
Processor = ATmega2560
Flash memory size = 262144
LFuse = FF
HFuse = D8
EFuse = FD
Lock byte = FF
Clock calibration = 56
Bootloader in use: Yes
EEPROM preserved through erase: No
Watchdog timer always on: No
Bootloader is 8192 bytes starting at 3E000
So to me it looks like the Controllers are actually there and good (but i dont know much about microcontrollers

still learning), so the Problem must be something more physical after all, some fried components on the board

Or am i missing something?
Maybe wrong fuse settings on the Atmega8u2?
What do they need to be set to?
I didnt find any information on fuse settings for the 8u2 on that board yet.
What else could i try?
Regards