Sorry to hear you are having problems. It is a new platform, so there is not as much information as other older platforms.
Hard to say exactly what problems you may be having, but this is how you set up for developement.
If you wish to code, you need to go back to the boot loader and flash the DEBUG-APP_Pemicro_v102.SDA file. However, it does not come up as a ulink, as Kiel MDK supports OpenSDA, and you should select this. You do also need the P&E Drivers as you noticed
The latest versions are here:
PE Microcomputer Systems OpenSDA
I also doubt you need to consider re-installing Windows in the future to solve these problems.
You may wish to consider Code Warrior if you are willing to use Windows. It has a very nice feature called Processor Expert that generates code. There is a learning curve to it, but it is quite powerful once you get the hang of it.
These are the directions from P&E for installing the Debug SDA:
1.Hold down the Reset Button (located in box #2 above) and then power the board by connecting to the USB port (located in box #1 above). You will notice the LED blink (located in box #3 above), indicating that the board is now in Bootloader mode. You can release the Reset Button at this point.
2.Open Windows Explorer and locate the "BOOTLOADER" thumb drive.
3.Drag the DEBUG-APP-Vxxx.SDA file onto the thumb drive (any application or firmware file can be drag-and-dropped onto the device at this point).
4.Remove and replace the USB cable. The Freedom Board is now updated to the latest firmware or application.
Also, here are some sample Kiel Projects:
http://cache.freescale.com/files/32bit/software/KL25_SC.exe