I would bypass everything in the fuel system. Run hose from the fuel pickup directly to the carb. No valves, filters or anything. That will let you know for sure that part works. The next test is a pain, but it will tell you a lot. You can pull the electrical box out of the 97 along with the harness that goes to the motor on the 97. Then connect it into your 96. You only need the dess, the power to the electrical box, and the start stop switch. And connect the 97 harness plug to the motor. You do not need the gauges connected. Test and see what it does.
Also looking at the thread, you never said if you checked the voltage regulator. You can just unplug it and test. You just can't ride for a long period of time. Do this before you try the full gray box swap.