Having looked at your source, and pinching someone else's IVTC, I came up with this. Checkmate removes the rain bowing and dot crawl very well. Other than that, the source is very clean. Such strong filtering like what you have used is just going to remove detail and smooth it too much.
Code:
MPEG2Source(vid_source, cpu=6)
AssumeTFF()
Checkmate()
Telecide(guide=1)
Decimate()
Vinverse() # probably not needed if using telecide's post-processing
ToonLite(0.2) # may thin lines too much for your taste
Crop(8,2,-8,-2)
The following is a good link for explaining some command line options for x264. I'm not sure if it explains some concepts in as much detail as you might like, but Google or maybe Wikipedia should be able to help you there. And you can always post questions you have.
http://ffmpeg.x264.googlepages.com/mapping