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To answer your question, provided the `99 is a diesel then the trans will bolt to your engine.
Now, `97 was the last year for the E4OD so the `99 will be a 4R100 trans., which is based on the E4OD.
I don`t know but it may be that you would have to swap over the solenoid block.
There is a guy on the pre-Power Stroke page swapping in a 4R100 to his IDI diesel in place of a E4OD, might be worth following his thread.
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