Achieving nanosecond accuracy with MKR Vidor 4000
No. You can't.
To achieve 1ns precision you need a 1GHz clock. That can't happen.  The MKR Vidor 4000 uses an FPGA with an &quot;A7&quot; speed grade. That means that (according to Table 20 here) you can't run at any more than 402Mhz internally (200MHz is all Arduino are rating it for).
Not even half.
Around 5ns precision would be the absolute maximum precision you could get if you stick to the Arduino clock specs.