How the USB connectivity will help here?
Magic trick, change something to something.
This is a hard-to-diagnose hardware issue online. 
Technically, it is a differential signal, it is slightly better at electrical noise handling, there is always a ground, and there are slightly more logs at kernel level.
With hardware GPIO UART, most probably there is no diagnostic information AFAIK.
Could you please explain ‘timer too close’ concept, and how it is related to data transfer issues?
In simple words, klipper consists of 2 parts, klippy and klipper.
The first is the Python host, and the second is the MCU firmware.
Python host tracks MCU time and schedules simple commands, like toggle this pin 5 times.
To make everything work, those commands should be executed in some order and at a specific time.
If the command arrives too late, it tries to be executed in the past. This is not possible, so the MCU does an emergency shutdown.
In your specific case, it looks like because of transmission errors and retries, the command arrives too late. There is no way to know for sure, but first, it is better to fix the network issue before investing time in something else.
There is the precise explanation: Timer too close