I was able to flash to the mainboard successfully but there was an issue with the EEPROM which I now know is an issue with the cable. However, in the time that it took me to realize this I did the CleanEEPROM.ino.with_bootloader.mega.hex and ever since I have done that, I can not connect to the printer via CURA. I initially tried everything here https://community.advi3pp.com/t/when-trying-to-flash-the-mainboard-the-computer-does-not-see-the-printer/55. I have tried flashing Marlin via Arduino IDE but I get the Error Message "exit status 1
Error compiling for board Arduino Mega or Mega 2560."
option enabled in File -> Preferences."
Some assistance would be much appreciated.
Solution: Ensure that the Marlin.ino file stays with the rest. Somehow mine got moved out of the folder.