I did a 68 Barracuda and I don't think you will be able to use off the shelf headers. Mine were custom made by Mike Roth of MR2 Performance (Lebanon, Indiana) as they have to be "snaked around" the gear box, torsion bars, starter, etc. I'd be surprised if any manufacturer had a set that will work. You can use the manual gear box but it will get hot (no big deal)as the header tube will be extremely close to it.
Mike also has the offset plate for your master cylinder which requires a modification to your brake pedal assembly. Mike can do that too.
Some minor modification to your right side shock tower will be required.
I'd be surprised if you can get everything under a stock hood without a scoop unless you are using a very low profile intake and then I would question the clearance between the carbs and hood. There is someone selling a Hemi Dart in the A body section. You might contact him and see what he ran into. My Barracuda is the second ad. Wish you all the best as these Hemi A bodies are a "RUSH" to drive.