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!