if the name has a junior e.g. Jose A. Ruiz, Jr. which comes first when the surname is asked first? Which is correct Ruiz, Jose Jr. A. or Ruiz, Jr. Jose A.?
Neither of those are correct, the younger Jose A. Ruiz would be listed as
Ruiz, Jose A. Jr.
if it was written in this lastname, firstname format.
He is the Junior 'Jose A.', so those names should be kept together.
Post-nominals always come after the name (as the word post-nominal might indicate). Thus a name Jose A Ruiz Jr, when listed surname-first, would be
Ruiz, Jose A Jr.
The same applies to names such as
Hammerstein, Oscar II
Runcie, R A K, DD MC PC