I can't help you with the communications issue specifically, but I agree thatIf you have other tools that will connect to it then they shouldn't have a problem. I don't have to worry about this because I have an 05 so I am emissions exempt which means no plugin 15 years or older.
I'm in MA. Inspections really aren't that rigorous at all, they just plug you in to make sure that your monitors are ready but you're allowed to have up to two monitors not ready IIRC. Those are easy to see via a scan tool.
Obviously if you have a fairly loud exhaust or you're totally slammed or have illegal front tint then you're asking for a fail, But I didn't have much of a problem getting my 05 OBXT passed with Tein coilovers and deleted resonator and mufflers. When you pull up to the shop, pull the inspector to the side and ask him if he's going to fail you or not they're usually straightforward and will save you the headache if the answer is yes.
On your downpipe though, if you can find a CARB number for it it might help to bring it with you but just having a cat should be good enough to pass. Sounds like you just need to go to a different shop man
-Justin
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