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Outside of programming the ECU to eliminate hardware errors for running MAF-less, and WOT spark advance / AFR / VANOS / etc., I suspect the tune has been altered in two areas:
1. The ECU has a transfer function for the intake, which should be adjusted any time the intake/sensors are modified.
2. Transient fuel tables, taking into account the advantages provided by the new intake setup.
You can try resetting the fuel trims, and watching your STFT on light load, then abruptly moving to WOT. Odd STFT with constant light load would indicate the alpha-n tune hasn't accurately accounted for the airbox (intake transfer function needs to be modified). If constant part throttle is good, but abrupt changes in throttle result in a high STFT, the transient throttle fuel maps need to be adjusted (tweaking these tables should only occur after confirming the intake transfer function is accurate).
A dyno tune is the ideal solution for either scenario, assuming your O2 sensors are giving accurate feedback. If they are old, I would replace them first to avoid spending big $$ on a tune when it's a sensor issue.
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