The 351 headers are routed differently since the block is wider. They have to snug up tighter to the block so they will match the h-pipe. If you have to modify the h-pipe my making the flanges farther apart to make them fit, you definitely have the wrong headers.
Oh, here's how much clearance I have (I hope you can see it. It's really rusty.
):
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351W 89 Mustang GT Convertible