Most likely the tune turned off the rear O2 sensors. If the computer has not been receiving data it will give the not ready or not able to read message. I am about to get a tune and intake, and I've put the question to Justin at VMP. Since I want to avoid the change out headache ever year, he stated he could write the tune to keep the rear O2 sensors on and the car should pass fine.
UPDATE: I reflashed back to stock and put the stock airbox back on. I guess the o2 sensors were being blocked by the custom tune. Everything is alright now and I got the sticker.
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-A7X- ~Stang Syndicate Boston~*2006 Torch Red GT*10/10/07 Performance:Borla FRPP Stingers w/ True Dual Midpipes, Magnaflow High Flow Cats, JLT CAI, Bama 93 Race Tune, Ford Racing 4.10 Gears, Nitto 555 Extremes. Visual: Black AVS Tail Light Trim, Honeycomb Tail Light Vinyl, Black Racing stripes, 35% Window Tint, Trunk Blackout Panel, Billet Antenna Delete, Mirror Covers, 17" Konig "Further" Rims, Quarter Window Louvers, 20% Tinted Head Light/Turn Signal, Boss C-Stripes, CS/GT C-Scoops.
2 years of MA inspections without issue. First year, intake and tine, second Saleen and lots of stuff.
But then again the station that passed me also passed my F150 when I knew I had blown back-up lights.
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2006 Redfire GT Vert Auto, every factory option, 490rwhp JDM Saleen SC, One piece driveshaft, Steeda ultralight springs - rear adjustable UCA and LCAs, CHE relo brackets, Granelli front cross-member, Intrax sway bars, Tokico dampers, Hawk brake pads, Shelby Redline wheels and Nitto tires, GT500 exhaust, FRPP 3.73's, Pioneer AVIC-D3 navigation head unit, and Saleen HID headlights. See profile for appearance mods