As far as I know I don't believe you can get a crate motor in a 289. You can get them in 302, 351, and some others. But someone correct me if I am wrong.
About rebuilding your 289, it would be just fine to have your 289 rebuilt. Your car might be on more down time because you would have to pull your motor and wait for a machine shop to clean it up.
You could buy a 302 crate motor, it would fit just fine, and then you would have less down time on your car.
There are so many different ways to go about it, it just all depends on how much money you want to spend and how long you can live with out driving your stang.
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