Interlacing goes a little something like this: 1080i50 is 25fps, split into two fields. One field has lines 1, 3, 5, etc. and the other has 2, 4, 6, etc. The odd lines are captured first, then the even lines 1/50 second later. On a TV these lines are dealt with correctly, showing odd lines, followed by even lines 1/50 second later. But computer displays don't deal with interlaced material, so they show both fields at the same time. If there has been much movement the picture will look rather odd. Google Image 'interlace' and see if this is what you're experiencing.
Your workflow is all wrong from what I can gather*. Capture the HDV tapes in FCP using Easy Set-up 'HDV - 1080i50 Firewire'. Don't attempt to change to another codec. When you have finished editing and are making a "master" go to a high quality codec, like ProRes. Make a smaller H.264 for YouTube from this ProRes file, making sure to de-interlace. Don't master in H.264 and then make subsequent versions from that.
Make this your golden rule: change formats as little as possible, and only use H.264 as a final format.
I only skimmed through it, but I'm not sure what you're pointing out in the YouTube video. There's the occasional stutter on zoom-outs, which is pretty normal on a YouTube video, and perhaps the pans aren't the smoothest, but there's no big stand-out problem as far as I can see. If it's just that the video isn't as smooth as it appeared in the Z1 LCD, you need to de-interlace blending both fields rather than dumping one.
Sorry if this is all a bit overwhelming, but I can't think of a simpler way of addressing it.
* Your workflow isn't exactly clear. Might I suggest you state your workflow again in clearly defined steps, being exactly perfectly precise, using the exact terms you see on your screen.