Opened file from Musescore 2 and can't seem to fix the formatting.

First of all, i know that in general MS2 scores are not designed to play particularly well in MS3, for whatever reasons. However, there is a whole book that I wrote in musescore 2 and I decided I finally wanted to be able to use it in musescore 3 as well. So I opened the file and braced myself to have to do hours upon hours of fixing formatting. ( For what it's worth, every single update seems to mess something up in the formatting of my scores, it's pretty frustrating but I've gotten used to it. My scores are method books for young kids so they involve a lot of spacing manipulation for ease of reading, graphics, etc.) So like I said, I was ready to go at it. But the problems that arose in the formatting don't seem to follow any logic now and without doing some ridiculous manual move-arounds (which will then save and screw up the formatting again the next time I update) I cannot seem to fix them by any conventional means. For example, in my old score i had changed the colors of some of the treble clefs to a shade of grey. The new score seems to interpret them as non-existent and replaced them all with black treble clefs, then printing my grey treble clefs a little bit smaller next to them. Fine, I changed the color of the new ones and started going through the score line by line deleting the 2nd treble clef on each line. Usually the music written after it snaps back to be closer to the new treble clef (having been displaced by a second treble clef), but not always. I have tried to reset any x displacements of all notes and measure lines to zero. This doesn't fix it. I tried changing the distance to the right of clef/key signature in style. This had no affect on the score whatsoever. You can see another example in my #51, where the measure of G's inexplicably has a huge space at the beginning of it. Yeah, I can spend a few minutes changing that by drastically moving around the X placements of everything, but that will save enormous displacement values for those notes and measure lines just to get them to look, in fact, evenly spaced.
Like I said, i prepared myself to have to fix a lot but was not prepared for my score to turn into a Frankensteins monster of displacements and manual formatting, that, lest we forget, will surely all have to be undone for the next software update. I understand, it was a musescore 2 score. But it doesn't seem reasonable that this would make it impossible to use in musescore 3. I appreciate any guidance or suggestions you all might have. If I actually need to rewrite the entire book from scratch, please let me know before I waste more time trying to fix this. Thank you!