First, please make sure you have the latest version of the software. If you need assistance follow the videos on the getting started tab of the Kinetis Motor Suite web page nxp.com/kms
KDS 3.2 with all of the updates
KSDK 1.3 Mainline
the missing elf file is due to the compiler errors you have. Your use of KDS 3.0 is what is causing you the headache. The projects for KMS 1.0.1 are not backwards compatible with KDS 3.0, plus the KDS 3.0 can cause a mass erase of the MCU.
Once you have these installed and the KMS GUI is pointed correctly at the KDS 3.2 install start a-fresh and use your newly create sequence.