Yes, you still have fuel cut with the Lexus/550, but really, that's a GOOD thing.
So long as you are running stock engine management, you want fuel cut. You want that protection in the event that something holes your IC, or you pop off an IC pipe connector, or even worse, your wastegate just gets stuck closed.
For the fuel pump, it should not be necessary, but it's a good idea. You've got a 20+ year old fuel pump in the tank, so a new one is cheap insurance. The AFPR is also a good idea. At the very least, you want to remove the J tube restriction.