Unless you don't mind check engine lights you gotta keep the stock ECU hooked up as much as possible. That means leaving the stock temperature sensors intact or else you will have to deal with controlling idle with the MS which is a pain.
The best way to do the fuel injection wiring is to leave the stockers hooked up stored in the engine bay somewhere so the stock ECU still thinks they are doing something. Don't cut stock wiring if you can avoid it, it makes the installation a lot cleaner. Find a spare fuel injector bundle connector at the junkyard and use that.
MS -> commandeered stock connector -> stock fuel injector harness -> injectors in manifold
