Modules are very sensitive to voltage fluctuations. They will shut down if voltage goes too high (for self preservation) and also shut down if voltage is inadequate (too low).
You may not be aware, but every time you disconnect the battery everything has to reset and that gets very confusing to the vehicle's computer (ECM).
If you feel the alt is part of the problem, unplug the plug and see if the problem continues or disappears. You can drive the vehicle a short distance with the alt unplugged and the worst thing is it will throw a charging system code and check eng lite., but you know it will go away after you reconnect the alt and drive a few times.
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If I unplug the alt. The headlights stop flashing but the check brake system remains and the brake light on the dash stays on. I am unsure of whether the high beam and turn signals return to normal.

 

Instead of a code reader you may need to use a scan tool to get the status of "Module health". If there is any module that isn't working correctly , it should indicate that..

 

The codes I got today were U0100 and a B1318 code. The b code is a low voltage code. And the other is a loss of power to the pcm or ECM. I'm strongly convinced the alt is the issue with it dropping voltage and causing the communication issue with the computer. Thoughts?