How to arrange rows selected in MYSQL query?
You are looking for ORDER BY FIELD(), and it looks like this:

SELECT 
  PK_ONE 
from 
  TABLE_A 
where 
  PK_ONE in (2,88,3999,4,282,33399,1,394)
ORDER BY
  FIELD (PK_ONE, 2,88,3999,4,282,33399,1,394)


FIELD() is a function which returns the position of an element (first argument) in a list of values (2nd, 3rd, ... arguments).

So you need to generate/template the list of values twice for this query.