Thanks for the responses. I went with a solution similar to Bandit's, securing the two pieces together with a single 1x2 /w studs on two sides at the very end of the shaft, since as there is not much force trying to pull the back end of the ship off.
And to try and clarify for AfolFree about building the shaft right onto the spine, the way that the shaft was designed made it so that the studs on 1x2 piece had to connect to both the technic spine, and the 4x4 plate /w 2x2 hole that fits on "top" of the 1x2, and since the two receiving pieces are at right angles to each other the studs cant fit in since the piece comes in at an angle to the two pieces. Sorry, I know that this explanation is confusing, but I can't thing of a better way to explain it.
Thank's again for the help and suggestions.