Just finished rewiring the internal power lines tonight. I have had some serious problems with digital noise in the headphone stage. The headphone amp drew power from the same board as the midi controller and other digital electronics reside on. I have changed this so that it now draws power from the card closest to the transformator. Also, I have re-added a 5v voltage regulator to the controller board and added a separate ground wire. I hope this fixes some of my problems.
While having the lid off I've also added the missing 500ohm (or actually dual 1k in parallell) pot to BD Accent, so now I thing everything except for the too-low samples/output levels are fixed. Fingers crossed, will test tomorrow!