Pontoon Boat Control cables for a 1997 Mercury 90 hp: Yes, your controls, electric, throttle/ shift and steering will work just fine. Mercury did not change the electric harness plug till 2006. The other option you have is to replace the powerhead on the 90 with a Mercury reman. See what the cost difference would be.
Don't forget, you will need to reprop the 40 for the pontoon boat.