What I'd do is flip the 97 motor and trans into the 98 car. Then get ahold of a 98 GTP pcm. Everything will plug in except the map sensor and the boost control soleniod. Pull out a solder gun and move the map sensor to the back and the correct connector, then add one wire to the harness if you want the BCS. If not..allow vacuum to control it.
You will also need to swap the passenger side axle from the GTP, as it's a little shorter for the HD transmission.
As for the vacuum being different on 97 vs 98-02, it's so little of a difference. 97 has a vacuum tree on the charger that feeds the bcs and fpr. On 98+ it's all from the port under the snout.
