Assuming the engine you built matches its description, you'd be better off swapping it in entire. Putting a nice fresh head on an old block often finishes off worn bottom-end components (rings, bearings) and turns the engine into an oil burner de luxe.

You will have to use your existing automatic transmission unless you're prepared to swap a whole lot more parts; the '65 transmission is shifted by two cables, while '66-up transmissions use a series of rods and levers. Everything's different: steering column, entire shift linkage, also speedometer drive/cable, driveshaft/front universal joint, etc.

In order to put the newer ('68-up) engine in front of the older ('67-down) transmission, you'll need a spacer bushing to adapt the larger crankshaft counterbore to the smaller torque converter nose. Last I checked, user charrlie_s on here has them.

You'll need to use the '65 oil pan and pickup.

Keep in mind, "Super Six" just means a 2-barrel intake manifold and carburetor and associated components (air cleaner, choke, etc). It's not a special/higher-performance block, head, or otherwise like that.

Unless your '65 is a factory A/C car, it has a rotating-rod throttle linkage, not the cable type required for the 2bbl setup. Addressing this can get complex and costly, because it also means different transmission kickdown linkage, the factory parts for which are now scarce and costly. You might want to go in a different direction to have a 2bbl setup, if that's what you want to have. See the parallel 2bbl setup article. Photo documentation of a very well done such conversion is here, and there's a nice pictorial on modifying a 1bbl intake here.

Pay careful attention to the carburetor mount pad angle. It's not supposed to be just flat with the top surface of the intake manifold; it needs to tilt the carburetor forward a bit, so the carb will be upright with the intake installed—the engine has a slight rearward tilt. 3° sticks out in mind, but that might not be correct; measure a stock manifold to find out for sure.

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一期一会
Too many people who were born on third base actually believe they've hit a triple.

Thanks for the reply Dan, I’ll try to get in contact with Charlie.

Just a FYI
I no longer have the adapter bushings. Member Greg Ondayko was having them made.

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Charrlie_S
65 Valiant 100 2dr post 170 turbo
66 Valiant Signet 170 nitrous
64 Valiant Signet
64 Valiant 4dr 170
64 Valiant 4dr 225

Hey update, I decided to swap the manifolds and use the kickdown linkage from the 1970s engine. The swap went fine, besides 2 broken studs, but they came off with enough persistence (and replaced). Anyways, got it running and driving again, and it feels like better acceleration. However, I think it has a major vacuum leak. When it's fully warm and I step on the gas pedal, it stumbles and dies no matter how gently I press it. Never had this problem with the 1 barrel. Sometimes, if it doesn't die when I accelerate, it runs fine after 1100 to 1200 RPM and up. I am using a Felpro intake/exhaust gasket, but I ordered a Remflex one to maybe remedy this.

Any thoughts on other vacuum leak sources or causes of this problem? Any suggestions on next steps would be appreciated. Ask me anything I haven't explained well. I am using the carb off the old engine without rebuilding it, however, I wasn't sure if I wanted to invest a 100$ rebuild kit into a carb that might have a throttle shaft leak. Thanks for your time.

I replaced the intake gasket with a remflex. Tried to start it up and drive it but it died trying to accelerate with the choke open. I took apart my carb and cleaned it put back together and tried again still dies when I try to accelerate when hot but it does idle Leaner than it did before around 3 1/2 turns out rather than 4 1/2 or so. Im going to replace the carb with a Holley 350 2300. I hear that the 500 is too large for most stock engines.