I have an 08 custom Sportster with a bad crankcase housing. I see a lot of older model engines on ebay. I was wondering if I could put my efi system on
say an 06 model that that was carbureted? or can I swap my heads to make it work?

 

Unfortunately, due to a difference with the EFI throttle body, the carbureted heads cannot be used with EFI without significant machining. You can put EFI heads on to a carb, but not the other way around like you want to.

You're stuck with the 07+ heads. Keep in mind that 1200 vs 833 heads are different for chamber size, so you need to match that if you aren't doing other motorwork or machining.