Hey Michal,
Thanks for the info! I am still receiving the same error after performing the steps you indicated with the USB-TAP:

I followed your steps to establish a debug connection in Code Warrior 11, saved the config, closed code warrior, manually ran ccs.exe, and loaded the config. Here are a few screenshots of the output and my FreeMaster configuration.
ccs.exe running with saved config:

FreeMASTER configuration per your screenshot:

A few questions/comments:
1. If the USB-TAP debugger is not regularly tested and I presume being phased out, then why are NXP and distributors still selling it? Seems like the documentation for these wireless charging products should be updated to reflect this.
2. I noticed that my FreeMASTER plug-in module selection is slightly different from your screenshot. Your screenshot shows "FreeMASTER CodeWarrior-CCS JTAG/OnCE Communication...". The closest one available in my FreeMASTER 3.1 installation is "FreeMASTER JTAG/EOnCE Communication...". Is there any difference between the two and why does my FreeMASTER plugin name differ from yours?
3. Since we need to run charging calibration in our final design of our custom board, we plan to use UART for communication with FreeMASTER. Can I reconfigure this project (WCT1000_A11_V3.3) to use UART to communicate with FreeMASTER? If so, how do I do this? It looks like QSCI0 is brought out to TP40 and TP41 on the Debug Board.
Edit. I figured this one out myself and got it working. Providing what I found worked for others to reference. Set the following:
#define FMSTR_USE_SCI 1
#define FMSTR_USE_JTAG 0
You can then use TP40 (TX from MWCT1000 to PC) and TP41 (RX to MWCT1000 from PC) on the Debug Board along with a USB-TTL cable. Then configure FreeMASTER as the following:

4. It appears that the FreeMASTER UART protocol is different from the UART command protocol I was told to use to read charging status information from the MWCT1000.
Example FreeMASTER UART command: 0x2B XX XX XX XX XX XX
Example UART command to "Read TX charging status": 0xFA XX XX XX
XX = Redacted information
The charging library UART protocol uses 0xFA as its SYNC byte (0xFA: for Master to Tx single command, and sync response from Tx to Master), whereas FreeMASTER uses 0x2B as defined by FMSTR_SOB in the code.
Question: How do I enable the wireless charging library API access via UART? I don't see the 0xFA sync byte protocol anywhere in the code or any hooks for such a protocol.
5. Maybe related to #4, is the WCT1000_A11_V3.3 code the same thing that comes preloaded on the MWCT1000 IC from the NXP factory? Asking to make sure I am using the correct code base example for production.
Thanks,
Derek