You want to find a way to make sure the PCM doesn't see a map voltage equivalent to around 19psi of boost with the stage 2. One way to do that would be a map clamp, however using a map clamp with a SAFC is useless since one would be overriding the other.
Increase your fuel pressure such that you'll be decreasing the voltage the PCM sees by "removing" fuel via the SAFC.
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