@flannelist has an excellent Wiki article on kernel panics, the technical term for the boot loop you are seeing. In it, they confirm that mic1 is located on the charge port flex, so your inclination to replace the charge port was spot on.
iPhone Kernel Panics - iFixit
What you're seeing is that the kernel scans its sensors every 3 minutes. If a particular sensor cannot be read, the operating system reboots the phone in an attempt to recover. The actual mechanism is called the I2C bus, which is a two wire connection between the SOC, or main processor, and the peripherals scattered throughout the phone.
In this case, the signal runs through the logic board to the FPC connector for the charge port connector. From there it travels down the flex cable to the microphone at the bottom of the phone. So if the signal is interrupted anywhere along the way, you'll get a kernel panic.
Typically, replacing the lightning port assembly cures the problem. However, if the issue lies on the motherboard itself, then of course changing the port won't help. Given that the behavior changed for most of a day, there's something odd going on, but it's hard to say exactly what that might be.
About all I can suggest at the moment is to check the big connector on the motherboard for any signs of bent or broken pins, along with any signs of small components next to the connector having been knocked off in the process of replacing the port. Although it's not a high probability, it is always possible you got a defective assembly that conked out on you early.
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Do you have the original battery still? Even though I don’t think a battery could cause these issues it can’t hurt.
da Duck