From the data you provided, the power supply failed(step2).one possibility: the connection between MB1166 and MB1248 is not good, or L1(On MB1166) is damaged, then in "C3, C4, C5" side you can detect the 5V voltage. 

You need to check the datasheet of the level shift IC, if it's possible, to check with the IC provider will be better or get a demo board to test before your design finalized.

This 24-pin connector is not a standard one to be compatible with LCDs in the market. you may choose a 6 bit RGB LCD, and develop a LCD shield.

CN1 is connected to PB14---- PB14 is the pin of STLINK MCU, means through USB connector(CN1), the PC talk to STLINK.

If you can try other IOs with the same actions you done?