To leeneia: Thanks for the feedback. I'll see what I can do.

The repeat pattern you've indicated surprises me: I've always heard it with the first, third and fourth couplets repeated separately. As for the second stanza being a chorus, it's often sung with verses paired (one is then either dropped or repeated to complete some pairing). That's why I was curious whether the second stanza was explicitly labelled a chorus. Otherwise, the verse stanzas are greatly eclipsed by the chorus (sung twelve times in total, while each verse is sung only once.) The shape-note songs I'm familiar with seldom do this, but then, Ingalls was writing for a different form of congregational singing, where not everyone (except the lead singers) would necessarily have been working with the music. Thus, the pattern could well have been that a trio would sing the song throughout, with the congregation joining in on the repeats of the "choruses" (whether a fixed chorus or a repetition of every other verse). Someone who has researched the performance norms of pre-shape-note congregational composers like Ingalls, Billings and Read may be able to weigh in here.

The middle line is unquestionably the lead, and I'm sure you're correct that it's written an octave higher than it's intended to be sung, so that your pitching in the MIDIs is right. I was mainly unsure whether it had been written with a treble clef or an alto (C) clef. It's one of those details that isn't preserved in MIDI files.

As for the original pitching, we can only guess (without the Malvina score); Ingalls, writing for voices, wouldn't necessarily have kept the same key, particularly if he was working from memory.

When you say LOUD and SOFT, do you mean f and p, or the actual words (presumably written above each staff)?

If scanning with a scanner/printer isn't feasible, a fallback some people have used is just to photograph the score with a digital camera held far enough from the page that depth of field is sufficiently flattened--this has worked serviceably even with tightly bound volumes. I don't expect you to do it at this point; it may just come in handy for you in the future.

Doesn't Noteworthy support an "Export..." feature? Often, music programs offer MusicXML as an export type rather than as a save type (the idea being that every save option should be very nearly lossless, whereas MusicXML as of yet only supports a notational subset).