Yep, I think you know now that you probably should have waited for the audio first, but if you right click on your audio track in PE, there is an option to allow it to split the track, but now that I’m writing this I’m not sure if that will split your clips. It might just create new tracks to move whole clips where they work better.
You might be able to sync raw video, export new video files paired with good audio and then online the new clips through media management.
Maybe you can use a demo to just see if any of this will work. Although, v4 seems to be even more buggy than v3 at the moment.
By the time you hassle with all of this it might be quicker to just re-assemble after sync. At least you’ve already made all of your decisions, so it should be a lot quicker than starting over.