You have quite a bit of options due to you having both cars
You can run the GSR harness on the car, but you'll still have to figure out the VTEC, knock, and IAB part. The LS doesn't have that on the shock tower connectors. I am not sure how easy that is to swap over. And since you have both cars on you, you might as well just swap it the OEM way.
The other option would be to use the GSR harness and use a VTEC subharness like one from Rywire that has the knock, and IAB connectors and connect it directly to the ECU harness.
Is your GSR running the stock intake manifold or a skunk2 type? Some wire lengths end up changing slightly do to the differences in sensor locations, but you can use the gsr stock harness. But if you are running a stock GSR motor, I would run the gsr harness. And if you cant figure out how to swap the shock tower vtec, knock and iab plugs over, just run the subharness instead.
My car is a 00 LS with a GSR and I am running an LS harness with a separate subharness for just VTEC. Since I am using the skunk2 manifold and hondata, I am not using the knock sensor or IAB functions.