I'm thinking about installing headers, while looking at different brands one said in foot notes "not for use with aluminium heads", which will be my plan at a later date. Wondering if other types should also state this.

 whats the problems involved in this set up, I know some alum heads raise the exhaust port, do they change between round and rectangle, maybe I should just wait til heads and headers done at same time.

 I already have slim pickin's on headers for a big block 1973 with air cond.. Now when I get around to new heads, will I be looking at custom headers? 

I have never seen a footnote like that unless they are refering to making them work with the existing AC system bracketry.

Yes some heads have raised the ports, but typically if they have done so they note which heads the headers fit or what port pattern they are configured for.