Why is our 1966 Plymouth Barracuda acting like this and how do you fix it????

My BF and I changed his '66 cuda from a 273 to stock 1bbl /6. Everything is brand-new or rebuilt. All new lines, hoses, etc. The only parts in the car that aren't correct for the year is the transmission, linkage and radiator. We used the radiator from the 273 and had it modified to work with the /6 (holes had to be moved for the hoses). The 904 A/T for /6 we bought on eBay and is from a later year; we sent it to Ft. Dodge Transmissions to be rebuilt and also had them modify the torque converter because of the crank shaft size difference. They had to combine the top half of the torque converter from the 273's trannie to the bottom half of the convertor from the /6. He decided to use cable linkage. The problems we are having is it overheats within minutes of running and it shifts slow, if it shifts at all. He spent all day yesterday adjusting the linkage with no luck. I read at allpar that the linkage from a 2 bbl carb will not interchange with a 1bbl.