Ya it really should run just fine right away. It may have adapted to run better in the condition it's in but as much as I hate to say it and as much as you probably hate hearing it, your going to have to tear back into it.
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1999 BMW 328i (Daily Driver) - m54b30 intake manifold, ebay headers, Rebirth Motorsports CAI, Rogue Engineering underive pulleys, Epic Motorsports Remote Dyno Tune, Custom 3 inch exhaust with Burns Merge, Schrick 264/248 Cams
1967 Buick Skylark - 430 Buick Big Block Swap.