Melodyne has been integrated with ARA into X3. Now you need only select the area you wish to work with and create a "Region FX" with Melodyne (Select an area, right click ->Region FX->Melodyne->Create Region FX). IIRC, I saw a post to this effect long ago, and think I remember that "Re-wire" is now replaced by this (but cannot recall the exact details offhand).
Edit: I believe the Melodyne installer also allows you to install the Re-Wire version, which is part of the Melodyne installer (there are options for 64-bit, 32-bit, Re-wire, etc.). I just checked X3 and I do, in fact, have the Re-wire installed, but never used it.