Check the flag in the output assembly that is triggered as each page is ejected. If this flag is broken, then the system will think that the output is full and stop operation. Have you done a complete sensor test through the diagnostics menu yet? You have replaced a lot of parts without stating you tried that first. I have never had a bad formatter trip this error and the sensor are connected to the DC controller not the formatter.
It may be a problem with the stacker. Do you have the original standard output tray that you could install to test? The output sensor is position "L" in the sensor test list.