MKV -> MP4 without conversion?

[MacinJosh]

First off, MKV is a fecking pain in my ass and whoever came up with it should be hung by his balls.

Ok, now that I got that outta my way, my actual point is this:

A lot of MKV files are H.264 encoded so I was hoping to quickly change them into Apple TV/iTunes compatible files. I've been able to demux an MKV into 2 separate files; ****.h264 (video) and ****.ac3 (audio). Both play fine separately.

Now I need to figure how to mux them into an MP4 container. Does anyone have a clue on how to do this? I've tried the following programs:

ffmpegx (absolutely useless program, very unreliable)
mokgvm2dvd (another useless program... out of my 3 Macs, it ran only on 1 and didn't do anything useful)

So, before anyone tells me to convert, I have. VisualHub makes excellent conversions but I'd like to not convert because re-encoding loses quality and a simple demux->mux or passthrough conversion would be much faster.