I had attempted previously to try and identify the values for each pin manually with a logic analyzer and colour bands same as Mr.Taka has attempted previously, but as we both suspect this leaves room for error. Additionally the assignments can change based on XR values for colour width and other settings so this makes documenting even harder when it is not certain which mode is active sometimes.
I tried another approach which maybe was already tried. I attempted to work backwards from the OEM display Citizen pin-out comparing the recommended connections with C&T for similar screens and take those as the assumed pins and then move forward to the TFT15 values.
On PCB V1 only line line for sure was bad. I noticed that usually RED was showing as Yellow, and Red+Green=Yellow, so I realized that one of the RED pins on PC110 has to be connecting to Green pin on VGA. Identified it as PC110#21 to VGA#25 (G2). I cut the trace on the PCB and I now had no cross mixing of colours, but they were still very wrong, likely because if misorder MSB to LSB as well as missing lines.
My approach purely from documentation and not practical testing leads me to believe that PC110#21 is RED2, which is consistent with the issue I was having.