Exporting Problems

So I have a heavily edited video that im trying to export.
It started off on my phone but it ended up being a vertical video, so I opened it in imovie on my phone and rotated it to make it horizontal. Next I uploaded it to youtube, (to get around the AAE file nonsense) and opened it in shotcut. I edited it, and went to export it, but it failed. Some examination revealed that it tried to export at it 25 fps 640 x 360 resolution. This makes no sense as my iphone is set to record at 720p 30 fps. (I have the video mode set to automatic. )
I changed the export settings to what it should be, and tried to export it. This time it worked, but there were problems. The audio effects and edits I had added happened at parts in the video that they shouldn’t have, they were out of sync. Additionally, some of my text filters were in a different place on the screen than they should be.
Clicking on the filters in shotcut made the text change to what it should be, but the filters and sound effects that I added were still out of sync.

Is there a way to fix this problem without re editing the entire video?

I am using 18.03.06 on my laptop running windows 10.

The file you got from YouTube, what are the details of that file?
In Windows just right click on the file, then Properties. Details tab.

file properties

360 resolution is 640x360
720 resolution is 1280x720.
In this example, this video is 1080 (1920x1080)