I decided to slow down on the squats given the knee problems that I was having but didn't know what to do with push ups and pull ups. So I decided to modify and did 2 pull ups followed by 4 push ups. My goal was 12 sets and I was pretty winded by the end. I did not keep time but I know I did the last 3 sets in a period of 3 minutes (checked with my music to be sure).
I did some light work on the knee that was bothering me including light bike work and near zero-weight leg extensions (for those I did about 25 reps spread over two sets and held at the top as long as I could).