Missing Step & Kickout Flashing / Sinking Front Step (?)
That's a bigger disaster than you see. That Hardiboard needs to be cut at least 1" or so above the roof surface. Believe it or not, Hardiboard can't get wet. It's the engineers' dirty little secret, can't wait to dole out the big fat "I told you so's" when the lawsuits begin.... 

That wet spot is your sign - you need to remove all the siding from the gutter on up, install step flashing, with the kick-out at the bottom you described, then reinstall the siding. You'll sleep better at night knowing it was done right, and it won't leak anymore.

EDIT TO ADD: I don't believe your stoop is related to the leak. May be a contributing factor, but not the culprit. Stoops are poured on ground that is disturbed and excavated during construction, on backfilled soil. Repeatedly, builders and homeowners pour stoops without firmly anchoring the pad to the foundation with steel to prevent reverse sloping. In your case, the stoop needs to be broken up, properly anchored, and repoured. Sorry.