Reformatting teacher duets into student-friendly secondo parts--the rests are driving me nuts!

I'm helping my old piano teacher rewrite teacher duets into a student-friendly format for an upcoming studio ensemble concert. See examples.
Original --> Winnie the Pooh - Secondo.pdf
The reformatted version:

As you'll see in the original, teacher version, both hands are written in the one clef. My goal is to transpose it up an octave and put each hand in a separate clef. Here are the issues I'm running into with what I've tried.
1. Upload the secondo/teacher duet file into musescore.
2. Go to instruments. Change voice to piano. Add staff. Twice to get treble clef, then delete the extra bass clef.
3. The new treble clef staff now has whole rests in all the measures.
4. I select all the whole rests and make them invisible.
5. Then I transpose the bass clef up one octave.
6. Then I select all the right hand notes (if I press shift I get the left hand too :/) and I move them up to the treble clef using the ctrl+shift+up shortcut.
7. Then I go change the stems to be facing the right direction. The selection issue I'm having from #6 slows this down.
8. Beyond small uploading and converting errors in the music, sometimes the notes come a measure too early. I solve this by copying and pasting back a beat, and adding the skipped note manually.
9. The main thing keeping me from continuing to reformat these songs like I've been trying is THE RESTS. There are some rests that remain behind, but transposing them or moving clefs doesn't get them in the right place, and neither does moving it with the arrow. Some rests can be edited or deleted, but with most, all I can do is make them invisible, and try the next thing.
10. I have 2 voices in the menu bar--not sure why. I select the voice for the clef I want, and then I select the beat I want as a note--not a rest, and I add a double sharp to it (so I remember that it needs to be a rest and that is isn't an actual playable note). Then I do my best to place the note on the count I want. It won't always let me, so I have to start by adding to the previous note as a chord. Then I unselect the pencil icon and click on those notes to convert. Then I press the rest key to turn them into rests. It usually looks okay, but, in the WTP rewrite above, you'll see that I have whole rests in the treble clef of measures 17-18 which aren't centered, and that bothers me. More importantly, it's insanely time consuming.

I'd love to hear better ways to fix the rest problem, and other issues I mentioned above that are slowing me down.

Lastly, I'm having trouble with making the measures and lines even.
1. I'm guessing that having the first line indented is the traditional convention, is there a way to change that?
2. Even my lines that have the same number of measures do not have the measure bars lined up evenly. How can I do that?
3. The last two measures (21-22) on the final line, are either squished (like in the image), or stretched the length of the line--only the two measures are not the same width. One will be squished and the other stretched--either measure or the other (you could flip-flop their width).
4. I tried fixing this by having only 5 lines instead of 6, and 5 measures instead of 4 in the third and fourth lines beginning with measures 9 and 14, respectively. However, the final line is still messed up. Measures 19 and 20 (1st ending) are squished to smaller than the width of the measure above it, and measures 21 and 22 (2nd ending) are stretched to the lenth of the line, the width of 4.5 measures above it.