Fox Header bolts not lining up after changing gaskets

Hey, I just picked an 89' 5.0 LX, my first ever project car, and I'm making my way through it. Just got a whole new catback put in yesterday and tried changing out the old head gaskets today. The engine's got a BBK SSI intake and BBK shorty unequal headers (pretty old and rusty) on it. I thought it'd be a simple swap but when I tried to screw the headers back on after replacing the gaskets, none of the bolt holes lined up with the header flange. I wasn't sure if I did something wrong or if these headers have just been so beaten and heated that they've warped and won't line up anymore. I don't have any tools that could make the holes on the flange bigger so I just wanted to know if I gotta bite the bullet and buy new headers or if there's anything else I could try. I've searched around the question quite a bit but haven't found too much that's useful. I'll get some pics posted later today. Thanks a bunch, any help would be much appreciated.
 
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I assume these headers were on these same heads before. If so, they should fit again. How did they come apart? Any excessively tight bolts (right to the end)?
 
Another trick is to take a couple bolts that are long enough and cut the heads off or you could use some all thread, install them on the end holes of the head, slide on the header and install the rest of the bolts.
After disconnecting the exhaust as mentioned above.
 
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