Did you figure this out? You can do this:
tell application "OmniGraffle Professional 5"
every group of every layer of every canvas of every document
But in practice you'll want to select certain documents. Run "every document" by itself, and you'll get a bunch of behind-the-scenes documents that Omnigraffle uses.
As far as order is concerned, a group contains a link to its canvas, so you could query its container hierarchy like so:
"canvas of every group of every layer of every canvas of every document"
More generally, I'd guess that item order (ie first, second, third) in Applescript lists correspond to Omnigraffle front-to-back order, and not the sequence in which they were created. This appears to be the case with layers (where layer titled "Layer 1" could actually be "item 2 of layers" in Applescript), but I haven't examined it thoroughly.