'65 Barracuda 318 LA Transmission Questions

If you get a chance to get an early Magnum;88 to 92,jump on it. These are pretty good building blocks. The decks are a lil lower, and they are born with higher compression, and "they say", the stock Magnum heads are better than any stock LA heads. An extra bonus is you can run LA heads on those early blocks, because "they say" those early blocks are drilled for rocker-shaft oiling, if you happen to have a nice set of LA heads.. A low mileage unit, could be a drop-in. If you never expect to run LA heads, then a newer one is, I suppose, better.And a supper bonus is the roller cam.
I say "they say" because I am repeating what I heard on FABO and have no personal knowledge. It is just an option.
About the only drawback to Magnums, is you will need a new intake, and an LA front end, if yours comes with a serpentine front. And "they say" truck blocks need to have the truck mounts slightly shaved to fit headers.
As to headers, if it was me I would get the type that pass a couple of the pipes thru the aprons, leaving more room in the tight tunnel;if it was me. With the stock cam. I suppose headers could be optional . But any cam with over ~40* of overlap, is gonna benefit from headers. By 45* you are sacrificing a fair bit of power and torque.
5.9 Magnums are, from the factory, already fairly powerful. And just by adding headers,a 4bbl,and fresh cold air; you might already by close to or over 300hp, and they are docile long-distance runners too. Just be sure to give them a free-flowing exhaust, especially the front half. Make sure you run it at over 180*; And I recommend working up to 200*, keeping up with the tune.
As to the transmissions;
The stock Magnum cam,IIRC, was a 252/112; so it has a fairly wide powerband. Therefore,I would gravitate towards the A999, or it's sister the A998. Both of these can be had with the 2.74-1.54-1.00 ratios, This 2.74 first gear could allow you to run a lower rear gear, for a lower hiway rpm, without sacrificing take off, as compared to the A904 with ratios of 2.45-1.45-1.00.... For example;the A904 with 2.45x3.55=8.70, while the A998 with 2.74x3.23=8.85. The rpm difference at 65 mph, is 9% lower with the 3.23s or about 265 rpm, if that matters to you. If not, then the early gear-set is a better fit, if you expect to swap cams later, or install any cam with a lesser LSA than 112.
By 1971 the A904 was pretty much perfected. But there is one better option . The early A998s IIRC, came with the A904 ratios, but had HD guts. But it also could be had with a loc-up convertor, which is maybe OK for the stock 5.9, but IDK if it would survive 300plus or for how long. So, IMO I would avoid a Loc-up A998. You cannot mix and match convertors; the inputs between loc-up and non loc-up are different; so get the right one the first time. Usually the trans type is cast onto the topside of the bellhousing, but "they say", not always. If not, then you'll have to figure it out.