Last time I've seen anything like this, cable used for emulating was dirty. Blew it out with compressed air problem solved, but I think maybe an offset issue. With the wrong offset you can verify the chip all day long and it'll report back good but won't work in the 'puter. http://www.gearhead-efi.com/Fuel-Inj...Flash-and-Burn
Also you're probably running off limp mode hence no sensor readings in TPRT. For some reason with PCMs, after resolving whatever problem it is, I could never get the CEL to go away without having to disconnect the battery.
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