If your comp introduces a lot of noise after adjusting the levels for the track, try adding a slight median blur. This should help, it’s gotten me out of a nasty track situation more than once.
I’m not a powerpoint expert by any means, I’ve only done a handful of presentations in it. That said, is the preview quality something that can be changed when you right click on the video or in the preferences? Does it look better when you export a final presentation?
I think you’re on the right track here. Map out your discussion and video. Find key areas where you would want to pause and continue your videos. Render your video in sections, then in Powerpoint or Keynote make the slides identical in design so there is no transition between slides. If the last frame of the video in slide 1 matches the first frame of the video in slide two, the presentation should be seamless to your audience.