The A4 is shifted by the PCM, based on throttle position, etc. If you alter the throttle body, you alter air flow vs. throttle position, and that throws the shifting off, requiring a reprogram. This is not an issue with the M6 (6-speed manual).
Might want to add a "signature" with basic info about your car - year, model, engine, trans and any major mods. That makes it easier for people to help you.
94 Formula A3+1: 381ci all-forged stroker - Callies Stealth, Oliver 5.85 billet rods, BME nitrous pistons / CNC LT4 heads / Comp Cams custom solid roller / TH400+GearVendors OD/4.11's / Strange 12-bolt / 300-shot N2O / Spohn Suspension / 6-pt roll bar with integrated SFC's / full AutoMeter instrumentation / MoTeC M48 Pro engine management system / a few other odds 'n ends. 800HP/800LB-FT at the flywheel.