OK, on the slant sixes that I've worked, I've seen both stud and nut and bolts on the inside hole which looked original, and the outside two were all definitely bolts, not threaded rod. The problem is finding grade 5 5/16 NC bolts with enough thread for the given length (in other words, the unthreaded shank portion is too long). Most of the fully threaded bolts you find are grade 2 or less. My solution has been to cut more threads on the requisite length grade 5 bolt. I don't remember the length right off, but I can measure and report back later.
The inside stud or bolt always breaks off in the exhaust manifold (I think maybe one time this failed to happen with me, but that was probably a stud that looked OK and I left in place), and you've got about a 50/50 chance on the outer ones soaked with penetrating oil, heated, etc. If you have not already done this, plan on lots of burrowing with a drill, tapping, rethreading, breaking taps or screw extractors off in the holes (I would advise not even bothering with screw extractors - you're pi$$in' in the wind with those) inserts, you name it, there will be lots of swearing involved, if you don't swear, have a heathen neighbor or buddy come by to do the swearing for you, because it will be a requirement!
D/W
Did that two weeks ago. Wound up taking the manifolds to a machine shop to have the center bolt hole drilled out and tapped. I also had the two manifolds bolted together and resurfaced to get a good flat face.