It sounds like you didn't optimize your media on import. Your camera shoots in a highly compressed aquisition format that should be converted to ProRes 422 for editing. So you invest the time when you first bring the media into your project, instead of rendering every time you make changes.
Larry Jordan explains it well here:
Ninety minutes is a lot of video. You're basically rebuilding the entire video timeline. Are you working with optimzied media or native H.264?
If you're going to be sending a compressed version, it might be better to make a master and use Compressor to encode, applying the timecode overlay there.