I use the SC-29 cord with an SB-400 on a D60. The cord extends all the hotshoe contacts so it works just like the SC-17 with the SB-400. You can keep auto mode or select manual with the flash off camera. One small advantage of the SC-29 over the sc-17 is that it has a good lock to keep the end of the cord secured in the camera hotshoe.
The IR illuminator function of the SC-29 cord does not work with the SB400. The feed for the illuminator comes from the speedlight not the camera, This feed is provided from two pins placed just forward of the hotshoe on the SB-900 or SB-800 flash. The SB-400 doesn't have these extra pins so it can't light up the illuminator on the camera end of the SC-29 though it can do everything else.
Hope this helps.
My own setup is an SB-400, SB-900 and two old SB-80dx's. I use these with a D60 that doesn't have the CLS commander function which is a bit limiting, so the SC-29 is quite useful. It lets me use the SB-400 off camera auto for a simple setup. It supports all the SB-900 features off camera including the remote IR illuminator if I want more powerful single light auto. Lastly I can take the SB-400 off camera on low power manual and use it to trigger the three more powerful speedlights all running in manual using their SU-4 remote optical slave mode. The SC-17 will do almost all of this for less money but the SC-29 is well made and I like it.