If the F_Panel connector is connected correctly, one end of the power button LED (Pwr LED) is connected (page 1-28). Check that the end that goes into the power switch is also connected. Also check that none of the wires to the switch are pinched or abraded.
The headphone jack is AC97 only. HD audio has a diferent jack and a different wiring scheme. Check the yellow plug to see if it is oriented correctly (page 1-26).
Power LED
Here is it broken out of it's shell. The light just doesn't come on. The wire doesn't appear mangled and as with the audio below the plug will only go one orientation so it's not plugged in wrong. The switch and HD LED which are the other outputs of the MB connector are fine and functional so i presume the leads are bust in an unapparently way or the LED is blown. Not sure how I can test this ...maybe a AA battery connect test. Im limited in the wire work I can do, don't have a soldering iron to fix it back if I cut it up...
USB connector
Internal extendor sounds good but have now realised I have no internal headersleft on the M/B. There was only one set (of 2 9pins) which is feeding the card reader front panel and the internal wireless compnent. Bummer! maybe an adapter for the internal USB 3 header argh
Sound
Well the yellow plug pin pattern means it can only go in one way so i believe it is plugged right.
The BIOS offers me HD Audio Controller as above with a Front Panel sub-option of HD audio or AC97. It doesn'y work in any of the 4 configurations here. Bit annoying!