The Ford manual describes special tool guide pins used for alignment #T71P-6049-A.  The two pins screw in where the head bolts go.  When the head is in place, the pins are removed and replaced with head bolts.  Not having these, I cut the head off a couple old head bolts and welded a rod to the top of them for easy removal.  Somebody here suggested an easier option of cutting the bolt head off and then slotting the top (this could be done fast with a cut off disk). 

This is how we do it in the shop on Detroit diesels,  we have 4 bolts that are the same thread size for the head bolts that are longer than the head and stick out.  the tops of the bolts have been ground down so the tops are rounded,  then the mechanics have placed them into a vise and used a hack saw to make the tops of the bolts look like flat screw driver style bolts.   we place the bolts into the block,  then (don't super tighten the bolts)  just enough to hold in place. Place the head over the alignments and presto. place in the rest of the real head bolts, and remove the stud finders.

cheers  hope this helps.