Ok, so I have it working. For anyone that's been having the same issues I have, I did the below and it worked.
On whatever version of the software you're using at the moment. Unplug the NES, select flash original kernel, follow the steps and hopefully you will have no pipe errors. Then delete your current installation. This should get you back to a clean NES. Then...
- Turn off Windows Defender (might not be needed but previously I'd transferred from a mac via USB stick)
- Download the latest version of the software
- Run the software again while the NES is unplugged
- Select the dump kernel option and follow the steps
- Unplug the NES
- Select flash custom kernel option
- Unplug the NES
- Add ROM's to the program
- Select upload selected games and follow steps
Hopefully like me you'll now have the LED turn off correctly once completed and your NES won't restart, hope that is of use to some people.
Thanks!