Just scored a Super Six and matching trans

Frank's right. The Super Six was the marketing name (and air cleaner decal text) for the North American '76-'82 2bbl carburetion setup.

1963-'69 Plymouths with 225 engines -- all with 1bbl carbs -- had "Super 225" air cleaner decals; the same engines installed in Dodges had "Charger 225" decals. These were not special high-perf versions of the engine...just air cleaner decals. See here for rated horsepower info.

The '66 auto trans will not work in your '65 unless you also change the driveshaft and use the '66-'67 speedometer cable, and you'll also need shift linkage and a shifter.

As for slant-6 speed parts, you'll hear the name "Clifford" come up, but be very careful before you decide to spend any money with Clifford. They have a long and ugly reputation for being a bunch of clowns; see for example here, here, here, here, and here. Much of what they sell is inaccurately described, and a lot of it is not even slightly cost-effective. The good news is that you don't need to go to Clifford to get hot rod parts for slant-6s; there are lots of other, better options. See for example Dutra Duals and header options discussed in this thread and this one, Erson custom cams, HEI ignition upgrade, Mike Jeffreys windage trays, Hurricane intakes, other exotic intakes. Hi-perf engine buildup here, high-perf parts and build info here.