So what format are the episodes with original audio?
The easiest method is to use two instances of VirtualDub at the same time; one with the DVD video and the other with the TV episode. Cut out sections of the TV episode file as necessary to make it exactly the same frame count as the DVD video, export the audio, convert to AC3 (using Aften), mux with the original DVD video (using Muxman) than replace the title on the DVD (using Vobblanker).