I have the expanded score and everything but there's one track I cannot find. It plays when Sam and Mikalah are first communicating with Bumblebee, and again when Optimus and the Autobots are at the dam and talking about the humans (shows Bumblebee being tortured etc).

It sounds like the track "Optimus" minus that flute sounding instrument. Does the track exist?

Here is the first scene with it.
YouTube - ‪Transformers - Sam talks about BumbleBee and eBay page‬‏ (http://www.youtube.com/watch?v=pREAC6oqSOs)

So far, there has been no sf/x free version available. And you're right, it's basically a version of "Optimus" minus the flute... More than likely even the same recording but mixed differently.

That's exactly what it is guys...

Daaaamn. Well at least we KIND of have it...