For the exhaust flange use an 18" or 24" extension from the bottom while holding the other end with an end wrench from the top.

I have never had trouble with the exhaust manifold studs, but since you still have an inch, you need a stud remover from the tool truck. It fits on a ratchet and has four round pins that are forced onto the stud when you apply torque with the ratchet. When going back together get some new studs, don't get the bright idea to use bolts. The stud is the only way to go in an aluminum head. Bolts are more convenient to assemble, but you will really have trouble the next time you take it off.

Leaving the intake in the car is far preferred in my mind because you don't risk breaking so many connectors and cables of all kinds. It also makes the head very easy to lift off. Some of the intake manifold nuts will have to be accessed from underneath with an extension and socket.

Good luck,