I don't envy you the task of deciding who will get the grants (and I say this as someone who routinely pores through hundreds of undergraduate student applications for scholarships and awards). Is there any way you can structure the MOOC to give you a cheap-but-not-trivially-gameable grade? That way you could formulate the "startup grants" as being awards for the best performers in the MOOC and cut down significantly on the administrative effort involved. Of course, you might want people to be working on their projects while they take the MOOC, in which case the timeline wouldn't work -- I don't know whether your MOOC is aimed more at preparing people for a startup or people currently doing a startup (this seems like a very important thing to decide and to be clear about).

... it occurs to me now that I've written this that you've almost certainly considered all the points I've raised already; but I figure I might as well leave them here just in case I've pointed out anything you missed. :-)