Bending is usually what it takes.
The long link that goes from the column to the trans will need to be removed from the car, and then you can straighten out the angle on it with a hammer and vise. Work a little bit at a time, and don't go too far with the bending. You'll end up taking it out, and putting it in, and taking it back out a few times before it's right. It should not take much to get it so it clears the header tube.
You will probably also have to adjust where that long link meets the shift selector on the side of the trans.