Welcome to the forum
It sounds to me like you have a set of car headers. Those will likely never work with the original bellhousing crossmember and with a manual trans. There is not a different bellhousing crossmember, they are all the same. Just get a set of headers designed to fit the '63-'72 trucks with a manual trans. The ones that are designed to fit are Hedman #69260's. The coated Elite series are #69268. Some guys will use the later model truck headers such as the Hedman #69090 or the Hooker #2452's. They are a litle tight with the clutch bellcrank, but they will work, have larger primary tubes, and are a little closer to a tuned header.
If different headers are not an option, you will have to change the bellhousing and trans to a later model style that uses a trans crossmember. Either that or go with an auto trans.