AFAIAC you are doing lots of stuff wrong.
For stretching, do a search on PNF stretching. It will build strength as it increases flexibility in those areas. Do this AFTER - not before training since if you do it right your muscles will be fatigued whcih will lead to injury.
For explosive speed check out Plyometric exercises. These are stressful on the body due to the impact nature. Don't overdue it.
For overall strength. Your sets should not exceed 10 reps. If you are not going to failure at the 10-12th rep, you are wasting your time. Ad more weight. A simple way to do this with free weights is get a dozen or so very small plates. 1-1/4lb. If you can do more than 12 reps ad 2 plates to the dumbell / barbell. USe that until you have increased your strength to do 12 of those then ad more.
3 sets minimum each exercise.
Like I said earlier, home workout. I don't have access to a lot of things right now, But I'll try everything I can with the highest amount of weight I can currently put on there ( 16 pounds ). But since even then, i still won't reach failure at only 10-12 reps I'll still have to do higher reps to get the same effect. I'm going to go pick up some new shoes tommorow, Maybe then I'll see about looking into some heavier equipment.
I'm taking all of your suggestions guys, It's helping, but everyone keeps saying i'm doing things wrong...but I've gotten results. My biceps for example have gotten compliments and I look pretty fit, even for a skinny guy. I can see my abs just fine without flexing, and I've noticed my calves getting bigger from the running/squatting. But my results have slowed down as of late, so It's probably time for a change anyway. I'll load up my app and seeing about changing up the routine.
As for the flexibility, i'll make sure to look that up. Maybe I'll do it on my off days instead of after the workout. The same day I go running.