Well then RIP, At least the rest of the game appears to be working correctly.
Did you try injecting SMT II? It also has a problem with intro. During gameplay thou the character icon appears right trough the text making it another glitch.
Did you managed to get SMT to work without any graphical glitches? When I tried your previous guide I managed to inject it but there is a graphical glitch in the intro where some parts of the screen are upside down and zoomed in.