I am afraid I don't understand your question at all.
CF Flasher was simple utility for downloading code to the ColdFire MCU. Are you looking for something similar for MPC5?
PeMicro offers their own debugger (called 64K Starter Edition of P&E's PKGPPCNEXUS) that will work U-MULTILINK-FX. Trial version is free (it is needed to be registered and logged in):
http://www.pemicro.com/downloads/download_file.cfm?download_id=194
Part of the package is also flash programmer PROGPPCNEXUS, offering similar IDE as mentioned CF Flasher.
In general I would point out following appnote:
https://www.nxp.com/docs/en/application-note/AN3283.pdf
or
https://www.nxp.com/docs/en/application-note/AN4365.pdf
Also following examples could be useful: