A Pitfall of Diversification

I've written five or six starts and created several different outlines for both a series of short stories and a novel and am wondering if I should write the stories and then try to connect them into a novel. I've presently got about 20,000 words on the go and 40,000 qualifies as a short story.  However, when you have 1000 here and 3000 there and they are clearly unrelated, it leads to some serious head scratching.
I guess this is what is meant by too many cooks spoil the broth - in this case, getting from start to finish of a storyline without waking in the middle of the night with another alternative whispering in my ear.