Great job RSM, best advice I can give is, chase the threads. After I tear Into a project like this I always get a tap and chase/clean the threads. Manifold bolts can be very contrary.

I know this isn't helpful now but if you are ever into it again, sometimes it is better to just cut the nut off the top of the manifold studs. Once you take the manifold off you spray the base of the studs with penetrate. I did it every day for 3 weeks on one. It ended up coming right out. Whether that was luck, I don't know. Manifold studs and radiator studs/ bolts. Guaranteed to break some every time. Pretty cool the shutters and linkages were on it. Pretty uncommon, and almost rare if they are not seized. Good luck moving forward.