1- I do tend to get really cramped/ a lot of pain in my stomach from running and maybe I should try slowing it down a little more just to see what happens.
2- I try and do 2-3 full body workouts( i'll go like monday wednesday thursday or something like that) . I'll do about 30 minutes of cardio whether it be on the treadmill or another machine and then i'll go to free weights for bicep curls and other upper body exercises. Then to the ab machine which basically assists you in doing crunches I usually have it at 70lbs and i'll do 3 sets of 10 reps.
Q1) if you get cramps, then yea probably run slower and try to get into a cadence with breathing, the greatest advice like others have said is start slow, you're body will adopt and soon the cramps will be gone.
Q2) Sounds like you are on a good track. I suggest that you do your cardio after your workout b/c I have found that when I do cardio before I am unable to lift as much. For abs, crunches are ok, the bicycle exercise is an awesome ab exercise, just google it and try it out. Also some other excellent ab exercises:
1. Pushups! - your abs stabilize you, and it also helps you build the stabilizing muscles in your back. Pushups are excellent and there's many variations. (like OutThere said, a great exercise you would not expect)
2. The plank -google it, great core exercise for abs and helps you lift more
3. The Side bridge -google it, great exercise for core strength and obliques
4. I find crunches to be inefficient, weighted crunches are ok, but I think that these exercises will ultimately be more beneficial in reaching your goal. I've seen people do hundreds of crunches a day for a couple years with the only result being that they are very good at crunches.
Like others have said, getting a 6 pack is some genetics, but you can get some great flat abs w/o a six pack and look great. But still
nutrition is still the key. proper nutrition is the difference between getting cut and lean and just getting big fat and bulky.
I cannot emphasize how important proper nutrition is. It will benefit you in reaching your goal and staying health the rest of your life. Most problems with weight/health are not solely b/c of the lack of exercise. The majority of these problems is from improper nutrition.
With your workout plan, it looks spaced well, are you doing exercises like squats, deadlifts, pullups/chinups? These are staple exercises and are great b/c they use so many muscles as you do them. The Bench Press is also a staple, but it can potentially lead to injuries so be sure that you are not trying to lift too much, remember than proper form with lighter weights is much more beneficial than lifting a bunch with improper form (and will minimize injuries). Also a great tip is to go to the gym or wherever you workout with a small notepad and record your exercises, sets, weights, reps, and such, you'll see some great improvements other than the size of your muscles which can be deceiving.
When you are more established in your cardio as well, I will suggest trying out some High-Intensity training, it'll help you carve out your abs and get more definition. But as the name suggest, it is very taxing on the body. So I'd suggest that first, you do as others say with running. Is your goal to be a distance runner for competitions? or just for overall health and improving your physique? in the future, High intensity training would benefit you in the latter once you are ready for it.
A key thing for all this is to be persistent and not give up, it separates those who want to look like someone who has a nice physique to being someone who is healthy, content, and has the physique that reflects that.
But it would've been better for me to stretch more (I'm a little better now) and have gotten reasonable shoes in the first place. 
