I think that the reason that you are not recovering very well is that you are doing both exercises both morning and afternoon and then throwing the Ruck on top of that. I think that you need to focus on strength training or endurance training either AM or PM.
I think that you'd be better off in the long run to just run in the AM and the just lift in the afternoon. Even then your not going to recover very well doing them every day. Your lifting needs a split where you working upper/lower or push/pull.
If you are doing burpees for 10 min straight you're in pretty good shape.
Monday-AM Warm-up; Run
Monday-PM Strength Training
Tuesday-AM Warm-up; Burpees, Jumping Jacks, Hill Climbers, Yoga'ish' stretch
Tuesday PM- Ruck Walk
Wednesday-AM Warm-up; Run
Wednesday-PM- Strength Training
Thursday AM-Warm-up; Burpees, Jumping Jacks, Hill Climbers, Yoga'ish' stretch
Thursday PM- Ruck Walk
Friday-AM Warm-up; Run
Friday-PM- Strength Training
Saturday-AM-Warm-up; Burpees, Jumping Jacks, Hill Climbers, Long Ruck
Sunday- Rest
For Running- One run needs to be hard and fast. I like intervals. Say run 2 min rest 1 min. You'll want to run faster than goal pace. So if goal pace is 7:00 min/mile you need to be running 6:15 to 6:30 min/mile for the 2 min. Start with say 10 reps. The other two runs need to be easy. Slower than goal pace(7:00) then you need to run 8:30 to 9:00 min/mile for 30 plus minutes working toward 45-60.
For Strength Training- You can do your full body workout each day. Work towards 100+ push ups and sit ups. 20x5 or 25x4 or 50x2(mix it up) Work pull-ups here too. You can keep your other stuff here as well.
For Ruck- You make this seem very important. Work on increasing your milage here. You have three rucks a week. Try to get to 8 miles Tuesday/Thursday then 12 on Saturday. Working toward 16 on Saturday.
And you were posting on here at 12:10 AM. Go to sleep!