1)It is best that the head is removed but as long as the porting is done to the exhaust side only it is of little consequence...just clean it out well.
2)3cm??wtf? there is about a half centimeter to work with...
3)it does make a difference but... you've got to do lots of manifold porting to match. here's a rule of thumb. for every minute spent porting the aluminum head you'll spend 10 on the exhaust manifold.
It's lots of work any way you look at it.
Well worth it.