At first look, I read that Altera wants you to use the carry_sum going forward, not carry. You go the auto_carry_chains = ON, and you also already have ignore_carry_buffers = OFF. Did you read the rules of use in the QuartusII help for the carry primitive? I don't use them, so the convoluted phasology didn't jump out as something you did wrong there either - but please read that yourself to get more out of it.
The wikipedia page on TDC talks about a counter for the stage after a discriminator. Would a more traditional counter work for this stage of your design?