Put together an autosplitter for Retroarch that splits on screen transition after all major and minor bosses, and on last hit of Pete. You can find it here for anyone interested: https://github.com/Johnny-Go/Autosplitters/blob/master/MagicalQuest3Autosplit.asl

If you are having issues with the autosplitter you could try changing line 22 to the following and see if that fixes it:

int memoryReference = memory.ReadValue<int>(codeOffset) + (int) codeOffset + 0x04 + - (int) libretromodule.BaseAddress;