I don't think that you will be able to do that through SQL as the "IN" keyword will go through each record in the table and check that its in that list, whichever order it is in.
The best way i can think you do it, is to run the same query and then use PHP to organise your results ie
$query = "SELECT * FROM mytable WHERE id IN (1002,1004,1001,1000, 1003)";
$result = mysql_query($query);
while ($row = mysql_fetch_assoc($result)) {
{
$array1[0] = $row[2];
$array1[1] = $row[4];
$array1[2] = $row[1];
$array1[3] = $row[0];
$array1[4] = $row[3];
}
to give you an array of the results in the order you require
Is that what you was looking to do?