So, the bolt holes won't line up? Is that the problem?
I want to say that switching heads won't solve the problem either. A bolt hole only needs to be off fractions to not allow the bolt to pass through. It can be off so slightly, that you can get the bolt through and into the threads...but it won't actually thread in. But when you move things around a little, it gives you that extra fraction of a MM to thread the bolt in. Assuming you are just test fitting the header by attempting to bolt it on with the collector flange facing up and towards the engine.
If that is the case, when you swap heads you will run into the same problem. It isn't as much as the holes won't line up...it's more to do with the angle of the header itself. If that makes sense.
Are these used headers? If so, you might just want to have a machine shop resurface the headers, then they should line up. I had the same problem with used headers once before, I had them resurfaced and they bolted on with no problem. Headers tend to warp slightly.