We will begin discussing things as they come to me in the retranslation. For now:
While in the NA version Belthasar simply states that he longs for Zeal in his pre-Epoch speech, in the Japanese version he directly states that he was building the Epoch precisely to take him home. Sadly, he died before he could accomplish this.
Nizbel confusingly notes in the NA version that "the great Nizbel was defeated here!" Nizbel originally was meant to say, "you can reach Azala only by getting through me, Nizbel...who came back!" He was triumphantly announcing his return.
Chapter 24: The Time Egg
Concerning the Nu who sleeps "beyond the flow of time," the Japanese version more directly states that time does not flow for this Nu any longer.
Though a minor detail, it is interesting to note that in the Japanese version, the Poyozo Dolls say "EXECUTING HIGHEST PROGRAM!" instead of merely "Executing Program."