It's not one of the fanfics on your list; more like a fancomic anyway, but I'd suggest Obsidian's Lament.

It's a Beast Machines photocomic that's essentially a sequel to the series. It's very good, has a few completed stories, and is ongoing - at this point it's pretty much a continuity of its own as each one builds on the last.

http://www.tfw2005.com/boards/showthread.php?t=126300