Are you using Avisynth MT i guess :P

Be careful with FF3dfilter dont abuse it or the image will be full of jaggies. Second QTMC convert it to 59.976 fps , are you using SelectEven / SelectOdd to put it to 29.976 progressive? This video is pure interlaced so it will never be very smooth like the original source if you deinterlace it.

Is better if you use

separatefields()
selectevery(4,0,3)
weave()

This come at the end of the script to convert it again to 29.976 interlaced.
Always work in Avi without compression i recommend you Lagarith.