A small update: Since the 97 SE cinema DTS was in 44100hz and synched to its original 24fps source, we had to convert it to 23,976fps and 48000hz. This was done by using the command line tool eac3to, which did it very nicely and it still sounds great.
After that, DJ has already synched both ANH and ESB. He synched the audio to the 2004 SE versions, since we use those as our reference to synch both video and audio.
Since all conversions and synching alters the audio in some way, we decided to go with encoding it to DTS-HD MA 5.1 for the blu-rays, to keep any loss in quality as minimal as possible.