Yes, the vin scanned must match the registration. In MA emission test is not require if vehicle is 10+ years old, but I know they still connect to obd2, my guess is to get vin infoScan the GM computer. Your Jeep computer will have several codes causing a fail. Your inspection may require your VINs to match so you’d have to figure that out.
Are you using a Jeep Cat or GM ?If doing the exhaust your self the magnaflow heavy metal universal cats are a good solution. I've used them on a couple projects with no issues.