Not just trying to drop ibs but build back strength

I recently injured my knee and gained over 20ibs very quickly. I was not able to keep up on my regular exercise and now that I am starting to try to get fit again I have found myself out of shape with a few extra ibs and a weak knee. I have never ate bad but my metablism has slowed down drastically. I have just started on a 1400 calorie diet that I try and spread out into 5 meals a day. My run is slow but I can go 4-6 miles 4 times a week with sprinting on the days in between. I really want to strenthen my core as well as my upper body. If anyone has any tips I would greatly appreciate them.