The Hilborn injector manifold in the Round 2 reissue '64 kit is from the '63 annual kits. One is included in the '63 convertible kit I have, and I'm pretty certain it was in the hardtop also. Not in the '64 kit are four pairs of very short, plated injector tubes that go with the manifold. Those are in the Prestige series '63 hardtop, and subsequent reissues of same. They're on the plated tree, on the side with the custom parts. The second-issue Super Street '64 (with the Woodward Avenue box art copied from a GTO ad) included all of the clear parts from the annual kits, including the light transfer bar pieces. The battery box was not included. Engraved headlamp detail was added to the grille, though in the kits I have seen the detail is "clocked", or not aligned correctly. This was corrected with the Street Rods series and subsequent issues. I used to think that there were two separate '63 hardtop tools; one for the kits and another for the promo/Craftsman kit. They are probably one and the same. The slide for the hood area would be different for the two versions (kit with separate hood, promo with molded-in hood). The engine, firewall, and some other parts probably got moved over to the '64 kits back in the day. When the simplified engine was later added to the Craftsman version of the '63, they probably altered the body tooling and tooled a new hood instead of looking for the original slide (which may not have existed by then). That would seem to be the most logical explanation...
All of the snap Javelin/AMX kits were '74s. Those were done in the mid/late Seventies after the last updates of the glue kit which used many of the same parts. I won't say all of them were the same, but every one of those snap kits I have seen was molded in dark green, and had Hurst mag wheels.
You wouldn't want to mix parts from the two...they are completely different platforms. The Cougar is more closely related to the '71-'73 Mustang. Those are unit body cars with leaf spring rear suspension, while the '72-'76 Torinos had a full frame with coil springs front and rear.
All of the Toronado and front-drive Eldorado kits include Oldsmobile engines. '65-up Cadillac V8 engines had the distributor at the front, among other differences. Jo-Han never tooled a decent late Cadillac mill (nor did anyone else, for that matter). The Oldsmobile engine's valve covers had no lettering or script.
Model Car Science ran a two or three part article on building a 1/25 scale Batmobile back in the day. I haven't got the issues (don't collect MCS) but if I remember right, the builder started with a '65 or '66 fullsize GM car kit, and advised readers to use one too. I think he stated that it really didn't matter which one you used as a starting point (Olds, Buick, or Pontiac) because so much of it was going to be reworked anyway. The conversion involved a lot of cutting, sheet plastic, and putty, but the finished model looked pretty decent. Some kid probably saw one of those articles, grabbed the closest thing that was available, and got to it. And probably had a lot of fun doing it.
The Round 2 MPC Cosmic Charger dragster includes a newly-tooled Potvin blower drive setup; that one should work, and taking those parts out of that kit won't leave it unbuildable. This won't be of any help unless you could track down the parts...AMT did include a similar setup for the Chrysler display engine in their '61-'62 Buick Special wagons. The same display engine and trailer were then used in the '63 Nova wagon. The Nova wagon was later butchered into the Boss Nova (using the Chrysler engine to power the car). Unfortunately the Potvin setup wasn't included in the Boss Nova because in that kit, the engine is right behind the driver, and that setup wouldn't fit. So you'd be looking for fifty-year-old parts. It wouldn't be tough to scratchbuild/kitbash a convincing setup anyway.
AMT and Revell/Monogram both overproduced on the kits, in addition to that there was a proliferation of diecasts alongside those. Then the bottom dropped out. There are exceptions, but once they went to the downsized cars in the early Eighties, you don't see a lot of nostalgia builds on these (certainly not as many as pre-1980 cars). I know a guy who was getting sealed Nineties kits for $1 apiece up until a couple of years ago. He'd resell them for $2-$3 apiece at a local flea market. I myself decided to pick up a couple of the early Monogram kits a couple of years ago. I got one of the first four kits (the red Buick Regal), sealed box, for something like $3 (not from the guy referenced above). That said, if you are into the subject matter, that's good for you because you can stock up for cheap. If you don't care for NASCAR but do kitbash and build street machines, the chassis parts can come in handy. The truck kits have a slightly longer wheelbase; those chassis can be fitted to earlier bodies instead of stretching the car chassis (not that that's tough to do). The engines in most of the kits I have seen are pretty decent, too.