My assumptions:
a) 001 = the first two "zero"s are reserved for the VF-1S
b) 013 = is the 3rd VF-1A which is a subordinate of 001.
How do we know it is a VF-1A? because it has "0" as the first digit
How do we know it belongs to 001's group? because of the second digit which is "1".
How do we know it is the 3rd "A"? 3rd because of the number "3" in "013"
c) Hikaru is 011 which means he is the first VF-1A under 001's command.
d) 101 = is the first VF-1J which is a subordinate of 001
How do we know it is a VF-1J? because it has "0" in the middle
How do we know it belongs to 001's group? because of the first digit which is "1".
How do we know it is the 1st "J"? because of the last number "1" in "101"
e) 102 would be the second VF-1J of the same squad.
f) 202 = is the second VF-1J which is a suborniate of 002.
With these assumptions, we can conclude: If a plane has "zero" as the first digit, it is a VF-1A; If the "zero" is in the middle, it is a VF-1J.