Bodyweight training - help!

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Hey all!
I've been developing a list of some body weight workouts I've been doing the last couple of weeks, and adding new exercises that seem to hit a new muscular area. This really took off when I got a set of dumbbells (they go up to 20lbs each), and added upper body exercises. However, now I have a problem where my list is far too big to be practical! Doing some exercises now leaves certain groups (such as my abs or the muscles around my knees) too tired to do some other exercises, leaving big gaps in my daily accomplishment list. Does anyone have any advice about where/where/when/what to cut? I'll share my log/list with anyone who wants to see, which includes exercises, reps, times held (such as planks of wall squats), and weights added. I'm hitting a bit of a wall here, so appreciate any advice!
My goal is to get a mostly comprehensive workout that focuses on arms, upper body, and core. I cannot yet do a push-up, but have recently done my first few knee push-ups. I'm also going to start running twice a week, so want to get two days when I can do hour-long weight/strength training exercises.
I'd be eternally grateful for any help/advice!