I recently pulled the heads on my 1987 GT V6 after coming to the conclusion that I have a blown head gasket. Prior to removing the head I had oil in my coolant and a leakdown test revealed a 60% and 30% leakdown in cylinders #1 and #3. Therefore I figured that the gasket must be blown between the #1 and #3 cylinders. However, I can’t see anything out of the ordinary with the head off. What should I be looking for?...

You may have overheated and warped the head, such that the gasket's not sealing right between 1 and 3... Or else somethings physically broken/cracked.
Of course, you MIGHT just have equally worn out rings on both cylinders...
None of these things are good, I know

It's rare that a head gasket is so thoroughly blown that you can see an open passage between cylinders. I have seen it, but it's rare. Usually you can see discoloration or erosion of the gasket, or damage to one of the gasket's cylinder sealing rings.

Cracked or warped head is also a possibility, or (bite my tongue!) a cracked block.

Swapped a 2.8 in a Corsica that had a cracked block. Oil in the coolant. Thought it was just a blown gasket. Pulled the heads and the rear drivers cylinder had a hairline crack about 1.5" down the cylinder---that was a drag.

Banzai !!!!!!!

I really probably shouldn't be posting on this, since I haven't pulled my head out yet (pun intended), but I'll just offer some food for thought, FWIW:

Think that one possible cause for coolant in the oil, is failure (or omission) of sealant that is supposed to be applied to the head bolts' threads. This is based only on reading the factory manual, thinking (ouch-! ), and looking at an old 2.8 block from another car - the threaded holes for the head bolts seem to be open to the water jacket.

Check the head for cracks especially in those two cylinders.

------------------

I think that it might be wise at this point to send the heads out to machine shop and have them checked