Kerry, I agree that Hooker would not have made headers for the Galaxie that featured the lower exhaust port. Besides, a four bolt pattern indicates a Cobra Jet exhaust port, which is not one of the lowered versions. The only possible conclusion is that the Dove heads have a raised exhaust port. It's too bad that they didn't raise the bolt pattern along with the port...
I would forget about using the side bolts, slot the top hole in the headers down somewhat and then use an allen head bolt in that position if necessary, and a normal bolt with a large diameter washer on the bottom position. Hopefully there is enough meat in the header flange to allow you to raise the headers up on the head if the top bolt hole is slotted down.
Good luck on the problem - Jay