I dont know if you're actually a hardgainer/ectomorph, or if you're just not eating and training enough. . .but, regardless, I think the following is a good place to start (and I can personally attest to their results):
For nutrition:
John Berardi is a godsend, and his massive eating reloaded plan kicks ass for gaining good weight:
Part 1:
John Berardi - Massive Eating Reloaded, Part I
Part 2:
John Berardi - Massive Eating Reloaded, Part II
ME Calorie Calculator:
John Berardi - The Massive Eating Calculator
For a good weight training regimen, I would try to incorporate multi-compound movements (squats, military press, pushups, bench-press, deadlifts, etc) and push/pull routine. . .not necessarily bodypart specific exercises or machines. I have had good results with Joe DeFranco's Westside for Skinny Bastards II:
DeFranco's Training - Westside for Skinny Bastards, Part II.
In terms of running, if you're trying to gain muscle mass, most ppl are going to say long bouts of steady state cardio (like what you're doing now) are detrimental. If you feel the need to run then incorporate 1-2 days of interval training into your routine. . . actually, as I look at it, the westside for skinny bastards does do that so there you go.
Also, if you want to bulk up the rest of your body, you're gonna have to lose sight of your abs for a little while. But if you eat cleanly and work out hard it wont be too much of a sacrifice and easier to lean up later on.
Basically, the bottom line is that you need to eat and workout more and do it in an organized manner.