I recommend releasing exactly what is on the discs. Provide the extra tractor beam, blast doors (and, what the hell, "we've stopped") lines in a supplement so that individuals (like me) can mix them in if it suits them. But if you're going to all the trouble to release the LD audio, it should be untouched.
To recap: 1) Were these digital or analog rips? 2) What all mixes are being provided? mono? 70mm? 1985? 1993? 3) Will they indeed be synched to mux directly with the GOUT M2V file?