Years ago, when I put a 427 in my almost new '67 Cougar XR7GT, I used headers on which the flanges had been cut off and swapped to an 8-bolt all-up-'n'-down pattern. I'd suppose the job wasn't done in a jig and, I, too, had a degree of trouble getting the bolts started.
Ultimately, I bolted-up the passenger side, tight, with the engine swinging from the cherry-picker, put the driver's side header in the engine compartment loose, and then lowered the engine almost into place. With that degree of looseness, it was possible to get everything started and then tightened. Make use of the slotted, notched-out lower middle locations and get those bolts well started before you hang the header on them. This helps to get the header in the right position to assist in getting the rest of the bolts in without interference.
KS