Humm... I don't use PJ64, since my computer is not powerful enough, but I played Zelda64 with UltraHLE, and the same garbled graphic happens in the menu(your second problem). The same does with SupraHLE.
Yes I have the same problem with the picture in the menu all screwed up. Unfortunatly I don't think there is any way around it. (Of course if you own the game on 64 you could always play it on there. )