I had that problem with the stock steering shaft, and actually machined some aluminum spacer "washers" myself. I believe I made them 1/2 inch tall and maybe an inch or 1.5 inch in diameter. The thing is, once I got them put in with new motor mounts, it was raising the motor so much that the midpipe was pressing against the bottom of the car. Without the spacer, there was maybe 1/8 inch clearance with the new motor mounts installed, so I just left it without the spacers. The headers vibrate against the shaft coasting on downshifts, but I'm not worried because the shaft AND the headers are eventually going to be replaced. It really was one of the last things that ruined my faith in BBK.
Long story short, put new motor mounts in it and finangle the parts as much as you can to get it to fit. The BBK equal length shorties just have clearance issues and there isnt much you can do about it.