YANK IT ALL OUT!!
I did on mine and have no problems at all. Those thermactor pipes that were bolted to the back of the head can be used to plug off the holes if you flip them over. But since you have the heads off I think you can just screw a plug in there because I think they are threaded holes. Just ditch the vacuum lines goint to the thermactor stuff.
As for the A/C do yourself a favor and get the Ford Racing A/C delete kit. It relocates the power steering pump so it would be where Ford would have put it if the car originally came with no A/C. You have no belt rubbing problems etc this way too.
I assume since you are doing all this yourself you know what you are doing and I don't take into consideration that just because you are new to this board you are new to working on cars (or even Mustangs). Anyway, if you have any more questions this is the place to ask.
------------------
Indiana Stangers Association
Buy your parts here