This is an ugly repair. akin to a very rusty frame rail or floor pan. Once you get past that, anything is repairable.
AMD is a popular sheet metal provider (I really like their stuff) and they make good stuff, but they manufacture in batches, and when a given part sells out, it can be a few years before they have it available, again. And considering the impact "global warming" may have on petrol vehicles, these parts may someday (soon) become unavailable and never return.
If you want to keep the manual transmission, and presuming it's a correct A833 transmission that could have come in this car, you will want to correct or "install the correct" parts for the conversion. The correct parts do NOT warrant (I'm pretty darn sure) the (torsion bar?) frame rail to be cut. But I don't have first-hand experience with slant-6 e-bodies.
Converting from the automatic tranny to a manual has been a common conversion on these e-body cars for many, many years. But I've never known there to be a need to cut the floor pan and/or cross members and frame rails as shown in your images. I'm guessing the perpetrator did NOT have the correct parts for the conversion, and "made do" with the parts they had on-hand. A common choice among racers who expect the car to "go to the crusher" after their tenure of ownership.
I DO acknowledge there is some cutting involved for the floor shift mechanism around "the hump" from an automatic to a manual trans, but I didn't think any of it crosses a frame rail.
One of the key ingredients I've seen for sale at swap meets past, was the clutch pedal assembly, typically cut from an e-body "going to the crusher."
Unless you have the knowledge "in your head" from prior experience, examining a factory original 3 or 4-speed setup on a big-block e-body will rank high on your TODO list.
If you're NOT set on the manual, and you may consider going back to a 727 automatic transmission, the "correct" conversion back to automatic tranny may be the easiest repair to set things right.
With enough study, patience, and $$$, you can set this right no matter which transmission you choose. I doubt any of us envy your predicament. But a genuine 1970 e-body car is a pretty cool thing, even if it once was a slant-6 car.
Why is a slant-6 car an issue? You may not know, but a big block `Cuda (a Barracuda that came with a big block originally) contains parts and heavy-duty structures NOT found on the slant-6 car. The good news is, the majority of these parts can be had, original or aftermarket, so if your pockets are deep enough, and your desire great enough, you can set things right.
P.S. these are really good photos framed dramatically to show where and how the cuts were made. Well done.