Need a method for synchronization of galvanically separated microcontrollers
Question 1: is there a method to do sampling correction/syncronization between the microcontrollers? Can you suggest a literature in this topic?


All STM32 ADC are capable of using an external trigger to initiate sampling.
You can distribute a 100 KHz clock and use that to trigger the conversions synchronously.
This is the easiest and most reliable method, often found in many data acquisition systems.
How to do this is described in the reference manual of your chip.

You may need to choose between starting a scan or a single conversion per edge.
See AN3116 STM32™’s ADC modes and their applications


  Question 2: if hardware redesign is possible, currently I am thinking in software solution, how can I put syncronization between the seperated microcontrollers?


SPI is also a synchronous protocol, so that problem you have already tackled. You can get 100 Mbps isolators for cheap. You just have to keep an eye on the jitter they have.



You could also try to make some synchronization happen by calibrating against the SPI clock or intervals. By doing some software PLL like functionality.
But I'm afraid you'll be going down a rabbithole that way.