Hey Eric,
For the non-position independent code:
I have unfortunately since modified my application quite a bit from the original example so I can no longer share it.
Some tips which helped me though:
First of all you need to compile your custom code to one of the memory locations so the linker file of your custom code needs to be updated as follows:

The independent code example however assumes the interrupt table was placed at location 0x00000000 and manually relocates it.
To disable this functionality simply comment out the following lines from the function below:

In the void Flash_Block_to_Update(void) function I set the old and new address to always point to block A
Using:
flash_new_image_address_block=FLASH_BLOCK_A_ADDRESS;
flash_old_image_address_block=FLASH_BLOCK_A_ADDRESS;
/*Add image header offset */
flash_new_image_address_block=flash_new_image_address_block+IMAGE_HEADER_BYTE_SIZE;
flash_old_image_address_block=flash_old_image_address_block+IMAGE_HEADER_BYTE_SIZE;
But be careful because in the Update_FW_Headers function the old header (which is equal to the new header in our case) is being erased. So to prevent this behaviour also comment out the lines seen below.

Some other tips (not sure if you have done these already):
- check if the custom blinking led code properly functions when normally flashing it.
- If you are using the 2 EVB using the gateway code simply replace one of the files provided blinking led binaries using the exact name (this avoids having to mess with the names in the linker files)
- Sometimes cleaning the application seems to help.
- A nice feature in the S32 DS is the ability to directly check the memory locations in the S32k chip. By going to Window->Show View -> Memory you can add a monitor at location 0x2000 and compare it to an objdump of the binary file you are trying to upload to see if the data is being properly stored.
Hope this helps!
I am guessing you are also not aware if their are other (open source) solutions for compiling position independent code.
Kind regards
Sebastiaan