Let it warm up it starts popping under the hood?

Hello everyone. I'm having some weird issues. When it's cold and it starts it starts fine no issues with starting. But if I don't let it warm up for 10 minutes and I put it in gear it starts popping under the hood. And have absolutely no power. I've also noticed even after warm temperature it has almost no power. I am changing my alternator this weekend because it's on its way out and won't keep the battery charged. (Brand new optima battery less than a month old.) And shortly after that started happening the transmission started jerking. It's had a transmission flush at about 100,000 miles. Yes, it's the 4l60 and I know they have issues. I have a cap, rotor, plugs, wires, cam sensor, new filter and seal for transmission on its way in. Napa didn't have everything at one time. Is there anything I'm missing?