Recommended MPEG Streamclip settings for export to FCPX-friendly format?

Hey guys,

I make movie mashups and I've decided to change my workflow a bit, was hoping you could provide some feedback.

Currently, I am converting MKV to MP4 with Handbrake using the default preset, then using MPEG Streamclip to extract the clips I need. This typically works, although sometimes I see a lot of choppy playback in MPSClip (and not in other players), and I'm wondering if I need to eliminate Handbrake from the process and rely on MPSClip to convert.

In short, what is the best practice for converting blu ray rips to a format that FCPX will work best with?

Also, the primary target for my work is YouTube, Vimeo, DailyMotion, etc., and they generally have the same requirements for videos:

Video
Codecs (in descending order of preference): H.264 preferred, VC-1 acceptable
Aspect: 1280x720 (720p) or 1920x1080 (1080p)
Bitrate: 2 Mbps minimum, 4 Mbps maximum
Framerate: 25 fps (preferred)
2-pass encoding, progressive (not interlaced, this is very important)
Square pixels

Audio
Codecs (in descending order of preference): AAC, MP3, WMA9, MPEG Layer 2
Bitrate: 256 Kbps AAC or 320 Kbps stereo MP3 (ideal), 128 Kbps stereo AAC or 192 Kbps stereo MP3 (minimum); 44100Hz

Container (file format)
MP4, AVI, MOV

Thanks!

If you want to maintain best quality, go with ProRes 422. H.264 or any other highly compressed Long GOP codec will show generational degradation quickly.