Hello,
When using Free Running nothing should be retriggered from an event outside the module in which you select Free Running as Retrig Source.
In the Random modules when in S&H mode, then (Free running) Clock will generate a new value according to the modules own Rate.
The Seq Start will retrigger a module where you have chosen it as Retrig Source, when you have the SEQ/ ARP running and trigger a note. Notes played by the SEQ/ ARP will not retrigger - only a incomming note will.
If you use the BINARY mode in a Random module, then that will work as a random trigger according to the modules settings right away for the module where you choose that Random module as a Retrig Source.
All other Retrig sources including the Random modules in other modes than BINARY will be the different kind of Rate parameters. That's the RATE set for LFO's Functions, SEQ/ ARP and Random modules except the above mentioned. The E1 and E2 Grain Trigg is both the Density parameters in each Sample modules Granular sections.
The Retrig Source you have selected for a module you use as a Retrig Source in another module will be inherited.
I can only suggest you try things out, as it will give you a better feeling and understanding.