I'm not really sure about this, but I imagine that you would want to do 3-5 sets a day, three days a week, for each exercise.
Each set should be around 80-85% of your max reps.
The numbers might be a bit off, but in general, that is how you want to train the endurance exercises.
Also, can you do a muscle-up yet? Because that requires a completely different training style.
You might want to change it to 1 day of total rest, if your body can handle it. Have the former rest day be something lighter than the other days, like just the upper body and mobility work, but no running or swimming.
I have no clue how to program swimming, but I have some experience with running. You are building a base, which is good, but how much of a base do you already have? 4-7 miles can be a lot everyday if you are just getting into running.
If you feel comfortable with the runs, then 1 or 2 times a week you could go for hard workouts.
These could be tempo runs, fartlek runs, runs where you go fast on every uphill you run, track workouts, and so on and so forth. You can get creative with these.
Considering the amount of swimming, lifting, and running you will be doing, I don't think that 3 hard runs a week would be a very good idea. You could get an overuse injury very fast.