Motion Tracking assistance
 

I'm working on a promo for a client and they wanted me to put footage I took of one of their performances on the windows of the Metro train as it goes by.

I say to myself, "simple enough, I'll just motion track it."
I'm using motion 3, and at first I did a simple motion track analysis, but I wasn't happy with the results. So from then on I animated each frame with a keyframe. The tracking is alright, just need a few adjustments, but the video is absolutely terrible. The video thats tracking seems to have distorted lines horizontally on the layer.

I tried deinterlacing it, but that didn't work, and tried a few other filters, which zero success.

Has anyone else had this problem, and if so, how do I resolve it. Unfortunately its a shot that the client really wants so I need to do it.
Thanks in advance.

Can you post before and after clips?

I do not use motion so I can only give general tracking tips.