Great tutorial!
Just a quality of life tip, when you are merging two tracks in 3mle, you can utilize the Export/Import buttons for MML. They are on the top toolbar next to Append/Remove Track.
Export MML from the "secondfile.mml" in 3MLE, the tracks that you want to merge with your main file. You'll only be able to Export 3 tracks at a time.
In your "primaryfile.mml" opened in another 3MLE instance, Import MML.
Click Append tracks (or Create New Document if you are breaking up an already merged piece into parts)
Select the instrument you want those tracks to be
Set the name
Import
Repeat until you have everything together (or apart).
I find this to be very quick and painless, though there is nothing wrong with doing Select All > Copy > Paste since I still do it sometimes, if you got a Violin part with 6+ tracks, it's very handy since you can set the instrument and just a few clicks, you got it merged/parted.