Did you preview your project in Shotcut by pressing space? Was it aligned there?
I’m not sure what you mean. If you mean there are gaps between clips, you right-click empty space and pick ‘remove’ like at 1:07 in https://www.youtube.com/watch?v=pXdgg3mGpec
If video and audio of videos are out of sync (lips moving, voice coming too late or too early), then this thread might help you: Audio Aligns With Video In Shotcut, But Goes Out Of Sync After Export