Hi Adam, yes as you found unfortunately STL does not actually contain within it any way to label the unit system that is used for the coordinates in it.

I would recommend contacting your printer / service bureau to see what their policy is. I'm not sure what is the most common but they may require you to use a certain unit system or you may need to fill out a form or something that declares it, probably something like that.

As far as checking software goes, from what I have heard the Magics software is kind of the standard deal for that: http://www.materialise.com/materialise/view/en/92074-Magics.html . I'm not sure how expensive it is, probably not in the "cheap" range though I would guess. They do have a "MiniMagics" free scaled down version though:
http://www.materialise.com/materialise/view/en/1248872-MiniMagics.html which looks like it has some inspection tools, just not any editing tools. So that could be a good one to try.

Also Deelip Menezes has just recently put out a new company and has some new software for RP stuff. That's at http://www.print3dcorp.com/ pick the Print3D 1.0 Standalone button in the upper left corner of that page. I haven't taken a look at that yet myself but I would not be surprised if there were some basic checking functions in there as well. That also has some kind of automatic price quote and submit type system.

- Michael