James, for personal health and safety reasons, you really need to take a step back and figure out the bigger picture of what is going wrong with your printer. Just changing things and trying again is NOT "worth a shot" when you have multiple problems, some of which could result in the generation of toxic fumes and a house fire.
Here are a couple points to consider:
1) The hotend fan should run 100% of the time the printer power switch is on. It is (should be) hard-wired to the power supply, and NOTHING you do through software, USB, or the front panel control should ever be able to turn this fan off. Since you said your hotend fan "didn't come on automatically", you have a wiring fault. This should have been a red flag to stop and fix before continuing with anything else.
2) The stock hotend heating to 350C(!) is multiply dangerous. The PTFE (Teflon) liner on the throat has a safe working limit of about 240C before it starts offgassing toxic fumes. Two red flags here are that Marlin should have shut the hotend down way before 350 degrees, and YOU should have shut the printer down well before 350 degrees as well, so two safety systems failed. You need to figure out why the hotend exceeded its temperature limits without the safety triggers stopping it, as hotend overheating faults are the cause of quite a few 3D printer-related house fires. It's not a pretty sight when it happens.
3) As @csorrows mentioned, you are now at the point where you likely can't print without replacing parts (the PTFE-lined throat). This downtime is the perfect time to go through your wiring with a magnifying glass, and triple-check that EVERYTHING is wired correctly. Test the heating. Test the thermistors. Test the motors. Test the extruder motor. And since your system is suspect, unplug the thermistors one at a time to test the safety systems. Test EVERYTHING before attempting a print. I know you're frustrated right now, but it's just not worth the risks to proceed without verifying that your system is operating correctly.