Problem calculating my calories burned

Hi, I'm trying to keep track of calories burned for a workout routine I've built up to. The original workout routine can be found here: http://sportsmedicine.about.com/cs/conditioning/a/012204.htm

I modified it slightly by not including swimming (I don't have access to a pool) and I'm not bicycling because it already takes me a while to complete the workout. Also, since I've had shoulder surgery, dips hurt, so I included more sets of pull ups.

Anyways I've basically gotten up to:

Upper body - M/W/F - (week 4 of Phase 2)
10 x 20 pushups
10 x 25 sit ups
5 x 10 pull ups

Running (miles) - M/T/W/F
3/5/4/5/2 (Week 2 of training Phase 2)

I start by doing a 5 minute jog to get warmed up and then stretch my lower body before doing my upper body workout. I break the upper body workout down a set into 20 pushups, 25 sit ups, and 10 pull ups (every other set until I reach 50). Then I take 90 second breaks between each set. Once I've finished the upper body routine, I take a drink of water and start my run. I'm new to keeping track of how many calories I'm taking in (started recording the data today) and burning, so any help on calculating how many total calories I'm burning on M/W/F with this workout would be much appreciated.

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