My plan is to not use the flip-out tray, and instead run short cables for usb power, usb data, hdmi, and headphone jack all out through the left side of the case in the area vacated by the left speaker. I'll either have the raspi sit on the desk next to the lapdock or stick it with velcro to the back of the display.
I clipped the usb head out of the lapdock and did my usb cable connections there. I probably wouldn't do it this way again though, those wires are REALLY small and difficult to separate.
Using a usb micro to usb converter and sacrificed cable I came up with this color cross reference for the data lines. I have not verified that it actually works yet but it appears that lapdock red should be tied to usb cable green and lapdock brown should be tied to usb cable white.
I need to pick up a smaller 3.5mm barrel jack for the audio, the one I used is from an old sound card and is a little too big to fit inside the lapdock case. The lapdock speakers are 8ohm 0.5W. I did test my barrel jack with headphones and it works. HDMI source was an xbox 360 (running through the lapdock of course). From the speaker connector I used:
Red: Right channel
Black: common for right channel
Blue: Left channel
white: common for left channel.
White and black are tied together as there is only one common conductor on the barrel jack.
I'm still waiting on a micro hdmi extension cable from ebay/china. After my difficulties with the usb wires on the lapdock side there's no way I'm going to try to tackle re-doing the wiring at the lapdock hdmi connector.
pictures:




