The only way you stand a chance of the intake clearing the stock hood is if you go carb. I know it is possible to make a 351W with a 95 cobra intake clear a 1.5" mach 1 hood, but you need to lower the motor slightly as well as trim out some of the bracing on the hood and then reinforce it. There was a guy in PA who had an 89 cougar who was one of the first, if not the first person, to swap a 351 into an MN12, and that is how he did it. To lower the motor, you can either modify the mounts and then clearance the oil pan so it doesn't hit the K-member, or you could also shim the K-member down. The second option is probably easier, but from a handling point of view that actually raises the cars center of gravity, so if you still want the car to corner nicely, you should take the time to make some custom mounts and beat on your oil pan to make it fit. As for making the custom mounts, the easiest and cheapest way is to just go to the local sporting goods store and buy 4 hockey pucks, then drill holes through the center of them and run a bolt through the lower plate, 2 hockey pucks, and the upper plate and put a nut on top if it. This will be solid enough to not let the motor move any, but the motor will actually be sitting on the rubber pucks so it will help with vibrations unlike a solid mount.
Mike