I am not going to tell you to quit running. You said you are (or were) a marathon runner, so obviously it is something you enjoy doing. I am sure you are aware of the health benefits, and if your knees can take it, why not?
And despite what some say, you can gain mass while running. I am proof of it, as is almost any soldier/marine who lifts. Just realize that you have to eat that much more to make gains.
At this point, diet is as much more important than work in the gym to gain weight. Eat, then eat some more, and then do a search within this site.
As far as gaining weight, yeah, it will make it harder to do that 300 PFT, but it will come. Consider doing your pullups with added weight, as your number of reps get up around 15, lose the extra weight.
Why not deadlift? A great all around excercise, it will help with the weight gain, and also the pullups.
Do a search; Zeb + Pullups for a good informative thread.
By the way, are you Marine, planning on joining, or just using this as a standard? Just curious. Hope all this helps.