With the alignment and balancing after setting up i went through the same issue.
Simple solution was that the only thing that changed for me was instead of a camera and an extension tube, when doing my initial alignment I had a diagonal and eyepiece, which was only a little bit lighter than the camera anyway. So I just balanced everything with the camera etc in place and racked out the focuser to within a mm of correct distance. Then did the balance and just swapped the EP and diagonal in. Still worked perfectly well.
I only do my initial 2 star alignment and first polar alignment using the Synscan routine using the eyepiece. After that I just use the cameras, phd and my auto guider to refine the PA and liveview from the camera in BYE to do final 3 star alignment. Using a simple red dot finder allows me to make gross adjustments in the pointing sufficient to get a star showing on live view.
If you don't want to use BYE (I think there is a Nikon version now see here
http://www.otelescope.com/index.php?...emium-edition/ ) just using liveview can also work although an articulated screen helps!
Malcolm