If you think it's more standard for NES titles then I'll go through the script again. I don't think there's a perfect way of handling it, though. I think I'm going to do it case-by-case.
Let's not be hasty. The fact is, I'm not sure how much standardization there is on this particular issue in the NES era, because the NES RPGS that have been localized seem to generally have the capacity to present longer sentences in dialogue boxes. I was kind of surprised how short the chunks of text in your Mother 1 translation were between input waits. I would have assumed that you could have included more complete sentences in between input waits given the size of the dialogue box.
If there is a severe restriction around how long a sentence can be, I'm not sure if there's enough precedent to determine standards on the NES. I never had to deal with this issue on the NES DQ games I worked on. I did have to deal with this issue regularly however on the GBC DQ Monsters game, where the amount of text that could display in the dialogue box was tiny in comparison. In that case, I went with the method I prescribed to you, and didn't mind the presence of sentence remnants on subsequent lines. I can't say I did a ton of research on how other GBC RPGS handled their text formatting, but I did look at a couple for a basic sense.
Going back to Mother 1, if you can in fact fit more complete sentences in between input waits, that's the route I would go. If you can't, I'd continue to think on it before making any big changes.