Sounds like you've started from the wrong base map. That image I posted above is from the base map for the RB25DET (this one, Pro_R32R33-113_RB25_VE.hr32r33-113).
Maybe load that base map and import the data from your current tune if its otherwise good.
It is plug and play, load up the base map and off you go.
Throw the stock MAF(s) into the bin and run an intake manifold vacuum/boost reference to the ECU.
Preferably to run it to an external MAP sensor.
Get a Haltech CANbus wideband.
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