Combining mp4s for iTunes apple tv 4

[Chris Newbold]

I'm completely stuck! Hopefully someone will find this interesting enough to help!

I'm in the process of ripping my Classic Series Doctor Who DVD collection to iTunes (for apple tv 4) via Handbrake. As some of you may know all episodes don't exist in the same format. Since I'm aiming to rip and combine various source files into one mp4 file 'per story' there are a couple of major challenges to this:

1) Some episodes may all be on DVD but earlier DVDs only have commentary tracks on specific episodes. Therefore I'm having to rip several files (using handbrake) and then combine them to create one final mp4.Obviosuly I'm then trying to combine files containing different audio streams.
2) Some episodes are not ripped from DVD but are downloaded 'reconstructions' of 'missing episodes. These are mp4 but different frame size/resolution and appear as 'movie' file types when i look at the info pane in QT7 (whereas the rips are 'Apple mp4' file type).
3) Studio filmed Doctor Who is PAL interlaced and some episodes which were recorded in this way but now only exists as film prints been improved using a technique called Vidfire which restores the interlacing and sharpens the picture. Although it may sound strange, since this is how they are supposed to look, I want to preserve the interlaced look. So I'm ripping in handbrake using the demob BOB filter which works a treat.

I'm using two methods to create my final files with issues with both. I've been importing the files into Final Cut Pro X, editing and then sharing. Trouble is even though my project settings are PAL, I don't know how to export a file and retain the interlaced. Every file I export ends up progressive. If I could crack this it would be the most flexible method, but i'd have to accept losing the commentaries on specific episodes.

Alternatively I've also tried combining the files in QT7 in order to export with passthrough (to preserve interlacing). However either the presence of the commentary track AND/OR the fact that some of the files I'm combining may be slightly different frame sizes (??) means I end up with some episodes with no video and only sound (i.e. as soon as there's a transition to a new mp4 that's a bit different, the picture disappears.

Anyone got any thoughts? Is there an easy Final Cut export method I'm missing (this would help me enormously with my Dalek Masterplan project -someone out there may know what that means!) or is there a way to standardise the files to combine in QT?

Attached is screenshot of two files types I'm trying to combine in QT7 that will give you an idea of the file differences.

Thanks

Chris

[Chris Newbold]

I now notice one of the files is mp4 and one m4v if that helps...