This may be a stupid question, but have you tried a different adapter?
Replacing the DC-in board would have been my next suggestion, but you already did that. At that point, it's starting to look like a logic board issue. We sell the [product|155066|logic board] for $600, but are currently out of stock. You could put yourself on the notify list for the part (see link), or search Google with Apple part number 661-3765.
Good luck!