Hi Mark
Thanks for your assistance once again, those settings were correct and the USB is now enumerating.
Regarding our hardware, unfortunately I was not able to get the USB working using any of the other clock modes ie. PEE even with the correct clock divider / multiplier to achieve the 48MHz clock....its just would not work. At the time (this was over 2 years ago) I settled for FEI as the USB was working, and that was enough for me to continue development with our application. I planned to return to this later when I had more time.
I suppose, I did not bother to research enough of your project and plunged right in hoping it would do everything I wanted it to do without modification....That's my fault not yours.
Regarding your simulator. I had some issues trying to compile on my work machine...the make file was failing with a generic error and I tried a few different uTasker projects I had on file and they both had the same error. Although I can compile and run the project successfully on my home PC. See below error..

At this stage, I can now connect using the KinetisFlashTool AND also my device config app, these are the some of the issues / comment I have thus far.
1. I discovered the uTasker project does not support all KBOOT commands, namely erase-all. there is also some properties that are not supported...no big deal, and are not critical for image loading, however the erase-all is.As a consequence I had to update my app, to use the erase-flash-region command which wasn't too much effort. After doing this I was able to load an image successfully with my app and the uTaskerSerialLoader running on my hardware. :smileyhappy:
2. I can also load an image using the KinetisFlashTool. Great :smileyhappy:
3. After flashing my board and using GO cmd from the serial loader menu to start my application, the USB no longer functions. It does not enumerate or doing anything. I can unplug/plug the cable nothing happens.
To configure the hardware from the app I use the USB-CDC driver not USB-HID, should that make a difference??
I suspect there is some issue with the clock configuration that affects USB after jumping to the application. The Freescale KBOOT performs some clean up operations before jumping to the users code, not sure if uTasker is doing something similar...but with KBOOT the USB works as expected after exiting the bootloader.
4. There is no timer that will exit the bootloader after a period of time and automatically jump to the users application?
The GO cmd must be entered from the menu or press a switch to exit the bootloader? With Freescale KBOOT it will exit after a set time if no command is detected on a peripheral.
In summary, point 1 & 4 I would expect to be standard with the uTaskerSerialLoader to make it truly compatible with NXP\Freescale KBOOT.
Not taking anything away from uTasker, but it's worth pointing out for others that maybe considering your project in place of the Freescale\NXP Bootloader and expecting these features built-in.
Regards
Jerome