I ran into that on my tranny R/R......putting the tranny in originally with no headers was a breeze...
Tougher to drop it and reinstall with the headers in place....the jack I have hads front/back and side/side tilt controls which made all the difference. Other wise one header would have had to come off.
Now thats in a Barracuda....not sure about in an a-body. But it stands to reason that it will be easier to do the tranny first.