Vertical justification

Remove the spacers?
https://musescore.org/en/handbook/3/breaks-and-spacers
And: Format/Style/Page->disable vertical justification

Arpeggios: add them to the upper stave as well, don't overstretch the lower ones (see measures 8/12)

You don't say what you want to see instead, but to me, you have way too much space between your staves on the second and third pages page. I would start by removing all vertical spacers as suggested above (right-click one, Select / All Similar Elements, then Delete). Most of the extra space on pages 2-3 comes form the prepggios that you attempted to drag between the staves, but tha'ts not how to do it. Instead, add the arpeggio tot he top staff, then select the bottom handle and press Shift+down. What you tried results in MuseScore adding extra space to prevent the very thing you wanted - the arpeggio to cross staves.