Hello @bcelikte,
If the code is generated well and the mot file reaches on the board, indeed there might be an issue with the execution order of some and the application can get stuck at some point. Are you running the same example I've sent to you in the mentioned post?
What I would do would be to start first testing with the gpio example from our toolbox just to validate the hardware. With this simple example, you should be able to test that the setup is fine, you have the right connections and the board works.
After that, I would try to check the FreeMaster. Again, we have a very simple example for FM. With this one, you can check if the UART connection is set right. Be aware that the MPC5744P rev E has different pins connected to the onboard USB to Serial, so please check the schematic.
Once the setup has been validated, consider commenting blocks until the FreeMaster connection works, and with this method, you can find the source of the issue.
Also, be aware of the bootloader usage. Please connect the FreeMaster after a couple of seconds after powering the board, otherwise, it will remain inside the bootloader. Try checking to see if the led blinks without the FreeMaster connection.
Hope this helps,
Marius