Moving several measures of notes up in the score

I have a very unusual score created in Capella-scan as an xml file. I have been opening, editing and saving it in MuseScore to clean up the descrepancies. I was very excited a few weeks ago when I found the Duration Editor plugin. However, it seems to only work for one measure at at time. The file I was working with has a serious flaw where after a time signature change to 3/4 in measure 59, Musescore somehow inserted a couple of eighth rests and moved all the remaning notes to the right. I was able to use the Duration Editor to correct some of the flaws (one measure at a time), but it does not move notes up a measure after deleting a trailing rest in the previous measure. I was able to slowly manually fix measures 59 through 62 but found it might be easier just to erase measures 63-81 and put them all back in. Is there an easier way? A seperate problem, the piece is also meant for a flute, SATB & piano but I am unable to change the Instruments, as they are listed as MIDI, all treble clef. Any help would be greatly appreciated.