The flash over JTAG application can be found on this Freescale site by going to the search page and searching for "flash_over_jtag". To save you the trouble, I've provided a link direct to the web page in question, where you can download both the executable and source, if need be. This is for the version 2 program; be aware that there is a separate page for version 1.
The web page where where you can download flash_over_jtag_v2.exe can be found
here.
---Tom