why do my dash lights and headlights flicker like a blinker?

Hi Dave. So we now have a battery that is two years old. It’s now at 60%charge as of two weeks ago. We also just replace the alternator a couple of months ago. All my lights still flicker to the timing of the engine (instrument cluster, clock, radio, headlights, basically all lights attached to the car). I don’t believe the voltage regulator is in the alternator. We’ve tested and replaced all necessary fuses. I was told by Autozone by a man that works there that the voltage regulator is in the ECM/PCM. That’s a pricy fix. And I get really good discounts. What if this doesn’t fix the problem? What else could it be? I’m trying not to take to a shop. I don’t want them to try and take advantage of me because I’m a woman. I’ve had a couple of bad experiences. I’m savvy with some things car related. I ran a warranty department for a large independent dealer for years. Oh, what I didn’t tell you the first time is upon start up the car hesitates and acts like it wants to stall. It does that in park from time to time. I haven’t noticed in gear. I appreciate any insight you can give me. Thank you so much for everything. I’m grateful!

I am still thinking alternator or wiring harness for the alternator -- or the relationship of the alternator to the concerns on the vehicle.