erockrph, your plan probably sounds crazy to most people, but I do think it will work pretty well. I have done some unusual things with split batches like this before, especially when it comes to partigyle, when I'm trying to jack up the second partigyle beer to something rich and flavorful (as opposed to sort of dull and lifeless, which is characteristic of the second runnings of any mash). So, I say, go for it. Looks like after those first 3 days, the second two mini extract batches will be a cinch to boil up and chill and get into your already fermenting beer. Overall it should save you a couple hours versus brewing two 3-gallon batches.