Erm... well I'm going to re-do this encode but without dropping frames.
I figured out why dgpulldown didn't work well when I tested going that route. Dgpulldown doesn't like interlaced sources and it seems that when I encoded the video, even though I deinterlaced, it was still interlaced.
meh.
Another reason why it didn't look good is that I used yadif to deinterlace at the time but that leaves jaggy edges. I like the results with TDeint much better.
This time I will be sure that it it progressive with TDeint as deinterlacer
The end result will be the same running time as the original once again but without dropping frames so no risk of adding stuttering or jogging.