I started officiating college in 2008 and I'm pretty sure both came in after I started. I started working umpire in 2011 and I know the iron cross started no earlier than that. If the substitution rule existed we weren't using that mechanic to communicate it.
If you don't believe me, go and check the 2004 and 2008 rule book changes
From page 7 of the 2004 book (Committee Action for 2004):
"3-5-2-e Snapping the ball no longer necessary when Team A rushes quickly to line of scrimmage to create a defensive disadvantage"
From page 6 of the 2008 book (Committee Action for 2008):
"2-2-4, 2-29-2, 3-2-4, 4-1-5 40/25-second play clock system instituted"