Welcome. I too had been a GM person for MANY years. My brother worked for their steering division so I got the employee discount. Then I started to look for a classic and found my way to the Mustang; just something about it...
Bought a '09 Malibu and then drove a Fusion Sport at a Barrett...
Sorry the shop manual pictures didn't help. The Mustang engine assembly manual I have didn't have a picture, so it was the closest I had.
I have the same air cleaner as ponyboy showed, but I have a 289; I don't know toos much about the 260.
That does seem odd that they don't line up. I'm assuming you can't spin the air cleaner around to line up?
I have a 64 Comet and Falcon Shop Manual. You air cleaner matches the engine drawing in there. What is hard to tell is if the snorkel is proper or not. It almost looks like it is too long...