I would just be careful about letting the oil pan slip around on top of the 2x4. You don't want it to slip a little, and break the seal with the engine block.
Like I said, I have read about many people doing this without a problem. It is just not ideal.
Did you get the nut off of the stud? Are you just having trouble maneuvering the header in to place? Did you loosen the nut on the drivers side mount?that may allow you to lift the engine a bit more. Watch your power steering lines, if you do that. It may be better to just remove the mounting bolts for the PS pump, and lift it up, and tie it up, so it is up higher than the mounting plate.
I am just throwing things out there, since I have no idea how much you have already done.
Good luck with all of this!