Are you sure that's coffee? Based on your earlier pics, it's probably smoker's tar. If it is definately coffee and never cleaned up, it's most likely corroded away parts of the motherboard and is not repairable. I'd be really wary even if you repair/replace the VRM that it will smoke out just as quickly once again.
Same goes with the video riser board - that's a fairly simple part (it just reroutes the video connector right angles, more or less), that shouldn't fail unless something is seriously up with the motherboard itself. Be wary. Cube motherboards are pretty cheap now, I'd consider replacing that before all else (+ VRM which looks toasted, I don't think that'll be repairable). Resoldering the things that have "popped" off the board will most likely release more of the magic smoke ... what has popped off (tantalum caps, and ?) is not normal for a plain VRM failure (usually it's the MOSFETs that fail on these, and just the VRM fails, not everything else going all toasty).