Dear John,
Amateur assessment and comment based on doing this more than once:
1) The photo suggests that you have Hall Big Bore headers
2) No surprise that they're not aligning with the exhaust port bolt holes.
3) I think you imply that you still have a pair of junk 4V heads.
4) Currently your good heads are on the block which is sitting in the engine bay.
I would suggest that you compare the mis-fitment of the driver's side Big Bore header on the good heads to the 4V heads sitting in the garage. If you're convinced that the mis-fitment is the same on both heads (it should be), then.......
I propose you take the header and the 4V head down to a competent exhaust shop. Explain that the header does not align with the ports and the exhaust bolt holes. Ask whether they can apply some oxyacetylene heat to the primaries and make them fit. If they can do this, then be prepared with some exhaust port bolts and be prepared to remove the header wrap. Also ask them if they can weld a rod or bar along the lower edge of the header flanges to tie them together once they're aligned properly so this problem doesn't happen again.
Once done, take it to the engine and confirm that all is aligned. Bolt it on with the exhaust gasket and confirm good fitment. I have had a set that required a bit of grinding of the bar to have correct fitment. Then you'll need to re-paint and re-wrap the headers.
I've done this more than once. The additional bar welded along the lower edge of the flanges is not readily visible and is obscured by the primaries, spark plug wire ends, etc.
Since I have adopted the welded bar, those individual and independent header flanges have *stopped* moving.
Warmest regards, Chuck Engles