Not sure if you solved your shutdown issue or not... Typically the PCM will de-energize the fuel pump and ASD relays for shutdown. ASD (Automatic Shut Down) relay typically feeds fuel injectors and coil packs. I'd start there.
At least this is the way it works for my viper engine swap... Good luck - cool build!
At least this is the way it works for my viper engine swap... Good luck - cool build!