A\C heater box vs non A\C heater box

hi all, sorry if this have been covered before.

i have a 70 Swinger, factory air. i recently decided to go for the American Autowire replacement wiring harness (510603), very nice harness so far, just one thing that i was not aware of until i called today and was told that the harness does NOT work with factory installed A\C, and apparently it is in the directions that it doesn't but no were on their site does it say that....Regardless i was not planning on removing all the air stuff (not sure if it is working, missing things) but i had to in order to get the firewall fuse box mounted. now for the real reason i started this...

1) is there a way to, hopefully simple enough, "change" the fan ducting to reuse the heater core part and not the "air" side that will interfere with fuse box? was thinking to reuse the vents and defrost for heat.
2) do i have to change the whole heater core and fan housing to a non-air unit?
3) or just go aftermarket for heat and a\c unit?

i see where lot of you guys are using aftermarket and seems as easy\simplest way to go, so i figured id ask


thanks ALL