I'm having trouble figuring out the problem. It seems that at first you couldn't do a pull-up at all but now you can do one from a standing position and have can kip yourself over the bar. That's fine, some people count kipping pull-ups others only use strict form, I mix them up. I'll kip on day 1 but use strict only on D2 and try my best to do strict only on D3. Sometimes I even mix that up.
So like, how many rounds could you get on L1D1. You say your biggest problem was endurance, well yeah, that's what D1 is supposed to train. I'm not sure what that means does it mean you couldn't do it at all or that you only got 5 rounds in 20 minutes. If so the purpose is to try to get 6 rounds the next week, and 7 the week after. That's what I like about Simplefit, it gives you concrete numbers to gauge your progress.
I think your homemade plan is a great start, only I'd do simplefit first and use it as a tool to gauge my progress. Like on Monday try L1D1 and whatever the number, record how many rounds you got, whether all pull-ups, or kippping pull-ups, or body rows. then do your homegrown schedule to help work on your endurance more.
I think you have a good start here, but the main goal is to keep you motivated and active. It's important to put your own fingerprint on your workout. Keep posting and let us know how you're doing.