Hello Erich,
If you compare ENET in PinSettings component from the GitHub project with what you get following your tutorial in KDS 1.1.1 for FRMD K64F board you will see quite a difference. In GitHub project all pins (except EXTAL0) are No pin routed. In the newly created project all ENET's pins have signals assigned (and one of them is PTC18).
I can the fix the problem with PTC18 pin in my minimal project (and the tutorial) by changing ENET 1588 timer 2 to No pin routed. I'm not quite sure what possible problems this might create if later on I would like to use ENET module in my project?
In my minimal project I do not have a problem with pin PTD4 but I'm sure you would see it if you followed your tutorial in KDS 1.1.1 (it seems to be related to LLWU channel 14).
Regards,
Piotr