Thx Pl4 and Zee for your quick replies and info I appreciate it. Rookie Mistake
I'm glad I kept all the mono wav files and just had to run them through again.I've completed The conversion of the Star Wars Trilogy Anthology Edition. This is my first project so I'd like your feedback as I'm sure there will be some areas in which I can improve. There are certain parts during the conversion that I found slight clipping but I don't think that could have been helped. I only added a +1 in the output gains and kept all the channels at 0 without reducing any specific speaker as I though each person could adjust it according to there preference through there own system, I personally like a lot of RS and LS.
Audiomuxer is a really great program as well and putting together DVD's was really a simple process once you got going and it doesn't take long for it to Mux as the program says!
Thanks again for your help. I will hopefully start working on the prequel trilogy next!