The "Write data to mouse" command no longer times out when there is PS/2 mouse, and instead adds the 0xFF byte to the queue, properly fixes the hang when entering into the P55T2S BIOS' CMOS Setup with mouse set to anything other than PS/2;
Removed the incorrect implementation of the OPTi 495 register 0x27 bit 7, it had nothing to do with A20, and the A20 stuck error was caused by the previously incorrect implementation of the 8042 output port bit pulse commands which is no longer the case;
The 8042 now once again correctly initializes with A20 Gate on.