I honestly don't know. Ford started using the CPS in 1995. The 3.0L output numbers changed in 2000, and it had a different intake in 2001.
For 1995, RockAuto lists Motorcraft DU57 and
Alternate/OEM Part Number(s): F58E12A112A2D, F58Z12A112AA
Then I checked the parts for a 1999, and got these numbers:
F57Z12A112A, F58E12A112A2B, F58E12A112A2D, F58Z12A112AA, ZZM120370, ZZM120370A, ZZM52035Y, ZZM52035YA, ZZM82035Y
F58E12A112A2D, and F58Z12A112AA is listed under the 1995, and 1999. Summit Racing lists the application for F58Z12A112AA as 1995-2000 Ford Ranger.
My educated guess would be that the engine would work. The worst case scenario is that if it didn't run, you may need to swap out the CPS from the 1995 block. But I really don't see why you would have to. It seems that the motor was unchanged from 1995-1999.