Superchips sells one chip for EEC-IV and EEC-V. Two basic EEC-IV and EEC-V differences: number of I/O and depth of monitored systems (mostly for emissions, but electric IMRC on EEC-V is a big change that I can think of, made possible by the extra I/O).
Both use the same type of EEPROM, so the phyical Superchip is the same. The code in the chip is different based on the PCM calibration. If you want to use a chip from an EEC-IV 2.5L Duratec PCM, you can use it in any PCM. However, it will have to be reflashed if you want to use it with a different PCM calibration.
Besides, I'd be afraid of using an "off the shelf" code developed for a 2.5L on any 3.0L, regardless of vintage or configuration. Better to get a custom chip, preferably one done on a dyno. Too much timing and you can blow things up real fast.