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With itb's should I have my fuel pressure regulator referenced to manifold pressure, since the vacuum doesn't change much? Or is it better to keep it to atmosphere?
Engine is 1uz v8.
Thanks in advance
I think you're a little confused. You have to remember that the injectors are still downstream of the throttle plates. Unless you're using upstream injectors (stand-off injectors).
The whole reason for pressure-referenced fuel regulation is to compensate for the changing pressure differential across the injector.
The vacuum will indeed change with an itb configuration, however it is typical with this type of configuration to leave the FPR vac line disconnected (referenced to atmospheric pressure). Compared to a plenum/single throttle arrangement, you'll tend to see quite a noisy map signal at closed throttle from an itb and this tends to make it harder to get stable fuel control at idle and light throttle.
Thanks for the info.