Jed,
It's important to match the intake manifold port sizes to the intake ports of the heads that you use. The stock cast iron and the Edelbrock D4B, 4 barrel manifolds match the port sizes and the mounting bolts to the '65 heads.
Another thing to consider is the vacuum advance from a 2 barrel engine distributor might not work with a 4 barrel carb., i.e. there might be too much advance at the higher vacuum of the 4 barrel carb.. Once you get it running, always check how much mechanical advance there is, using a timing light with a dial to read the advance at higher rpms. Then connect the vacuum advance and read how much advance it gives at higher rpms. Don't let there be too much of advance; stay within the specified limit for your engine with a 2 barrel cam. My service manual for the 273 with a 2 barrel, lists the maximum vacuum advance as 10.5*-13.5* distributor degrees at 15" vacuum. Remember that crank degrees are 2X distributor degrees. I found that with a new vacuum advance (supposedly correct) there was way too much vacuum advance and the engine would stumble and not run at higher rpms (too much advance and preignition). It runs fine with only the mechanical advance which gives 19*-20* (crank degrees), max. advance. On an automatic, static timing is 10* BTDC, so I get 29*-30* (crank degrees) total advance with just mechanical advance. With a manual transmission, static timing is 5* BTDC (crank degrees). On Mopar vacuum advances, there is an adjustment screw inside the vacuum nozzle for an Allen wrench. The amount of vacuum advance can be turned down by unscrewing that screw.
I hope that helps you to get it running right.