You should have two from original extruder or two from spares bag. Anyway I would not skip. You can try printing but nylon is tricky. I haven’t tried.
M3x20 should be fine if your motor threads are deeper. But 18 tip should not be flush. Check that head is fully inserted (flush) and not blocked somehow.
I assume you mean the heater wires (red) because the thermistor wires (blue) should not get hot. Anyway, did you angle the heater block as indicated in steps 12 and 13? This will give extra space. That’s how I have it. You can put the heat cartridge in the other side to have the wires on the right but that puts them close to pinda and risk calibration issues. But I did run that way for a while without obvious problems.