I recently bought a dash wiring harness for a TA with the digital dash to put in my car. BTW, I have a 1987 GTA. Anyway, when I went to pull the dash, much to my surprise, the wiring for the fuel pump didn't run all the way back to the connector that is behind the rear seats. I always thought that's how all these cars were. It seems to me like the wiring for the fuel pump plugs into something up by the dash, then runs to that connector.

The new wiring harness does have the wiring that runs all the way back to that plug, but it doesn't appear to unhook anywhere; it looks like it's part of the dash harness.

Is this something that is different between cars that originally had analog gauges and cars that came from the factory with the digital dash? Would it be easier to try and find where it would connect up by the dash and make that work, or just pull the carpet and seats and run the wiring the digital harness came with?

There was a change in the design of the wiring harness that occured around 87 & 88. My Guess is that you got an 88+ harness.

On the earlier cars the fuel pump wiring ran to a "intermaidiate" harness that also had wires for the fuel gauge, and tail lights, as well as any rear options ( power hatch, 3rd Brake, defrost, ect.) This plug is located behind the drivers side kick panel. On the other end; The intermediate harness then split off and the fuel gauge/pump wires ran to the hole in behind the rear seat & the tail light wires plugged into a connector for the rear tail light harness at the back of the car.

Around 88 they did away with the "intermediate" harness. The wiring for the rear options, fuel pump/gauge, and tail lights was intigrated into the dash harness and ran from behind the dash to the area under the drivers side rear seat arm rest trim. There the fuel gauge/pump wires ran directly to the hole behind the rear seat and the tail light and options wiring was plugged into the tail light harness.

That sounds like your best plan of attack !