You can cut, rotate, and weld the upper intake to make it a easier to run a FMIC, but it isn't necessary. It kinda depends on which IC you decide to use. Mine:
Any kind of porting/cleanup work you can do on the intake, head, and manifold is going to help you out power wise. Remember, increase the air flow and you increase your power. And a word to the wise, don't cheap out on a head gasket. Get a good one the first time, it will probably save you some time down the road.
Some swap from an internal wastegate to an external wastegate claiming it prevents some boost creep. I wouldn't worry about an external gate unless you are going to some monster turbo and lots of boost.