I've seen elsewhere on this site about the changes to the heater box when doing a Small block-to-Big block conversion.
(http://www.camaros.net/forums/showthread.php?t=110403)
I was also going to add AC (maybe a Vintage Air system) later in this rebuild.
My question is: Will I be wasting time or money getting a big block heater box and core now and doing the AC later? What, if anything, does the AC system replace in the heater assembly?

Yes, you will be wasting your money on unused parts. If you are thinking Vintage Air, go to their website and download the instructions. This will show you what you need to keep and buy.

X2 on that. I was set to order the same parts then realized that the Classic Auto Air system will negate some rather large parts. That works great for me because I want to use headers on my 454 conversion. I have read that a 69 Camaro with factory air/396 combo, will make the installation of headers very difficult, if not impossible.