Bad formatting

I suggest that you put a note in your version 2 scores that they need to be used with version 2 for best results. It is easy to have both versions 2 and 3 on your computer at the same time. Version 2 is not deleted unless you delete it yourself.

Are you selecting the option to reset positions on import? Try declining. This gets most of it back. The remaining problem are the texts you had placed directly over the notes. I downlaoded one of your scores and see you used rehearsal marks for both types of marking. That's too bad, it would have been better to have used different element types - or at least different text styles - for the different kinds of markings. In the future, I'd recommend using either staff text or lyrics or string number for the circled markings below the staff, and then either some sort of Symbols (press "Z" for that palette) or fingerings with a custom "User" text style) - for the markings placed directly over the notes. Then you can simply set those two styles to work as you want by default, no manual adjustments needed ever again. But it's too late for the scores you've already created using rehearsal marks for everything, unfortunately.

For the particular score I downloaded, it actually works quite well to simple select all rehearsal marks (right click on, Select / All Similar Elements), then uncheck "automatic placement" in the Inspector. So, in a matter of seconds it looks just like it did in MuseScore 2.