Flickering lights on my 1998 Honda Civic ex, why?

All my lights on my car starts Flickering when I'm on the freeway(sometimes), when I turn my car on in the mornings(most of the time). I went to autozone to check my battery and the alternator, and said my battery was not good so I changed it but I still have the same problem. I also checked the fuse and it's good also. I don't know if it has something to do with the engine or transmission because my car has over 200k mileage and you can feel the transmission or I assume it pushes forward itself sort of but it doesn't move, it feels like a bump. Like it hits something inside the engine. Also one more thing, my car lights deemed when I step on the break. Does anyone have any one have an idea of what might be wrong with my car?

My guess is a loose wire connection or damaged wire. If all the lights are flickering in the same pattern it might be on or near the alternator. Vibration and wind from the freeway and additional vibration from a cold engine could cause the bad connection to flicker the lights.