Electronic – DIY car audio noise when the source device is charging from the same power source

There a few things missing here. Maybe too many questions for a comment, but maybe enough to help you see where it's going wrong.

First of all, a 200mV peak to peak signal on 2.5V will give a range of 2.4V-2.6V, not 2.3V to 2.7V. Unless you mean it's 400mV p-p or 200mV amplitude. We'll assume you are dealing with a 400mV p-p 1kHz sine wave, since the other wouldn't work except to measure noise.

When you say a timer starts to measure the frequency, are you just seeing how long the signal is above your 2.61V reference? What are you expecting to find? A 314ns pulse from the comparator? Or are you just waiting for next rising edge of the comparator? What time resolution are you measuring at? What's your calculation?

Does the comparator have any hysteresis? If so, are you accounting for it?

Do you have any code for this project? Can you show it to us?

You should know that your method will only work for pure tone signals and it is very susceptible to noise. We don't know your ultimate application, so it's difficult to suggest alternatives.

The solution was to physically separate the power connections for the audio components. While @Dave mentioned in the comments something about a star ground topology, the problem was that while the ground connections were all centralized, the Vcc connections were also, and shouldn't have been.

In the original design, power was supplied to the entire assembly via a small PCB with header pins for each separate component. Two rows of male header pins, one for 12V DC and one for ground. In this arrangement, all of the noise was being dumped onto the audio components each time the servo motor was actuated. Adding capacitors helped slightly, but certainly not enough.

The main two wires supplying the small power distribution PCB are about 10 cm long. I added a second pair, and created a second power distribution PCB. The original one was used for the servos and receiver, while the new one was used for audio and amplifier. The "Y" split in the power cable ultimately had the effect of keeping the power clean on the audio side.

I also removed the ground connection between the RC receiver and Arduino, though this was unnecessary. Its presence did not add noise, nor did its absence cause triggering problems.

An electrical engineer coworker advised me that it was important to have separate power supplies for motors versus digital components. While this project still only uses one power supply, the solution was to split the power as early as practical, and dedicate each to its respective purpose.