355 Tubi Exhaust and modified Bosch M2.7 injection system?

Why do you think you should get a warning? The ECU will not care if the valve is present or not.

 

As far as I know, only the items marked with an "S" will generate a fault light (CEL) on the 2.7 car.

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Modern systems tend to throw a code at any controlled device that does not operate as designed--anti-tampering...

Oh Wait ! {{keyword: modern}}

 

Running the engine either with the valve open or deleted under conditions where the valve should be closed causes unmetered air to flow through the central piping rather than in the lateral piping where the two lambda sensors are located, thus cause the engine to run richer.
I have done the test several times and my conclusion is that deleting the valve or blocking it open is a no.

 

When did you discover your engine was running rich? If you disconnected your battery to work on the relay panel (for your Check Engine Light not working issue), you would have erased all faults from the ECUs' memories. ref: https://www.ferrarichat.com/forum/posts/150055052/
Also, you discovered some corrosion on your RH ECU wiring harness plug (41051). Maybe that was doing something strange to your engine management system. Those corroded pins control power to a lot of components.

Maybe do an ECU re-learn after you fix up your relay panel?

(EDIT: of course, it could be due to what @Timmo was talking about).

 

With a twin flow muffler (e.g. Tubi Evolution, Capristo) outside "fresh" air is drawn in and flows upwards the cats though the lateral piping, and the resulting highest O2 concentration will be picked up as a lean running condition by the lambda sensors and the ECU will instruct enriching the mixture, again under steady state running conditions where closed loop fueling is active AND if the valve is blocked open or has been deleted.
When the valve is still present and works as intended the fueling switches to open loop when the ECU instructs the opening of the valve and what the lambda sensors then pick up is not used by the ECU, at least not to adjust mixture.

With a single flow muffler (e.g. stock, Tubi R) which causes the known exhaust flow loop to occur I am not sure if any or to which extent outside air is drawn in, but it is not hard to imagine that this may also affect normal closed loop fueling.

 

ABS (Figure 4) here for 2.7 (Teves)

https://www.dropbox.com/t/Xjmm7sgI1hf9Jl2Y

Instrument/Handbrake (Figure 5)

https://www.dropbox.com/t/VRVsWGi0yCsiqMmL

HVAC (Figure 6)

https://www.dropbox.com/t/IQ1ZklvsylrrftHa

Suspension (Figure 7)

https://www.dropbox.com/t/2comMFe2urERE5Cy

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Well you have no secondary cats or bypass valve. You may or may not have primary cats.

If you're "sure" it's running rich because your exhaust smells like fuel, that's unburned hydrocarbons due to the absence of catalytic converters and rather high overlap oem cams.