I'm pretty sure stock 8.1 manifolds will hit the frame in a few spots on a square body frame. But you can go with any other stock 7.4l 454 manifolds from any year prior and it should be good with clearance issues.
So with that being said, you can go look all over the internet and find results of headers vs manifolds. Headers will always flow at least a little bit better than stock manifolds will (how much more depends usually on the price tag of the header). So in your case, since you need to buy manifolds or headers no matter what, you just need to decide what you care most about and how much you wanna spend.
For me, I went cheaper headman headers. Sure they're not the best, but they flow pretty good for the time being and got me on the road for the last couple years. In the future I'll probably redo the exhaust and go with a nicer set of headers. But for now it's fine.
I totally understand your desire not to "booty fab" things together with this and you want to do it "right" the first time, but in my opinion, try not to get into the "might as well" mentality too much and start spending lots of money in places where it's not a big deal if you change it later on. Exhaust is one of the easiest things to change on a rig later on if you don't like it. With a project like this, I say you do what you need to do, to get the thing running and working. There will always be another year after its running of working out the kinks and changing a few things up to get it even more how you like it. Just my $0.02 is all