I currently have my 86 460 pulled from my truck and I am currently reassembling it, though I have run into a snag plugging the holes on the back of the heads. I don't know what the pipe is called but it links both heads together and if I remember correctly it linked into the EGR, though I might be mistaken.
does anyone have an idea on how to plug the holes?

 

Easiest way is to bend the thermactor air pipe over and weld it shut (yes it's the thermactor pipe)
That way you are using the factory bolt and thermactor tube end to seal against the head
If you throw that term around much, parts men other than Ford boys will think you a bit odd
You could just say you need an air pump tube rear head to head like this one pictured below

 

 

You could tap the holes for a pipe plug if you want a cleaner look
There is hot exhaust gas behind the holes so your pipe plug must seal good
The one way valve atop the pipe keeps the two separate (air from the smog pump separate from the exhaust gasses)

 

What I did is put a pipe cap on the nipple that the valve screws on to. Just make sure the pipe itself is in good condition.