I've been playing through both MTI and MTII in SNES9x, and have come across a handful of bugs in MTII.
Most notably, the Royal Castle teleport bugs seem to prevent completion.
Would you be able to post your save file so that I may try out these bugs? It's likely that I did not account for all possible cases of the teleports, though I had only tested it by enabling and disabling locations in memory. I'd like to run through your save and see what I missed.
The "Divine" name had a missing tag at the end, so it ran over into the next entry. That will be a simple fix.
The shop dialogue, I had put placeholder text since I thought I had pointed all of the text to the correct location. I was obviously wrong and will have to re-investigate that.
The shop items seem to run over because I had miscalculated the length of the name "Metal Boots". This is actually a good reminder for me to go back and verify the item lists. I had changed a few of the items' names, and forgot to adjust the way to display them properly.
Thank you for the report, I will try to have these fixed and release a newer update.
*Edit: I believe I have fixed all of the issues except for the Royal Castle one, which I can't seem to replicate on my machine (though I'm actually noticing other problems with it now as well). If you're not able to post a save, could you tell me which locations you had unlocked?