Two issues:

1. The jeweler doesn't give a ring box as if he already introduced the rings to me.

2. The Maku Tree hints on the second dungeon, skipping the first.

How do I go about fixing that?

That is unfortunate, but it's nothing I can't ignore I suppose.

I don't know if this has to do from having some interactions deleted, but on occasions the next screen I move to is completely blank, or scrambled (that one happened in town). So should I just label it as a bad rom (even though it's verified as being good), or did it happen from deleting some interactions? If I want to rid of some interactions, should I simply adjust it because deleting altogether may glitch some things?