the tiny rubber piece at the bottom that fits over the spark plug didn't come up with the rest of the boot.
can I just put the old boot onto the new ignition coil or do I really have to replace the entire unit?.
You'll have to dig that boot out with needle nose pliers - don't risk reusing it, because it may already be damaged and could cause spark plug arcing.
O'Reilly's has the spark plug boots (includes the plastic tube and the rubber boot on the end) for about $10 each. You just pop the old one off of the ignition coil (don't lose the spring), and pop the new one on.
If the coil is good and the rubber is good. Re-use them.
You should replace the coil itself too. The boots should come with new coils. The ones from autozone did anyways. $12 each.