huh, it's interesting that you brought this up because it does leave some gaping holes. I mean, the second time around, Melchior used the dreamstone to create the Ruby Knife, and it became the Masamune when it was stuck into the Mammon Machine, though you think it would have already been termed as the Masamune due to Masa and Mune being infused in it. UNless there are two completely different ways to make it and Melchior made it differently the first time where there was no Ruby Knife stage.
As for Gaspar, I just kind of figured that with all of the people coming through the portals that some of them helped build what we see at the End of Time and that Spekkio was some ancient God of War that had managed to wander through and test whoever came along, in search of the ultimate challenge. I mean, the former makes sense because Gaspar would have had to help whoever came through, and he did say that there were others before Crono and Co., which means that there were other incidents when 4 or more people came through. Helping them get back to their time period may have instilled in them a need to pay Gaspar back and they could have just as easily came back, once they knew how.
As for the latter, Spekkio might have just as easily been a warlord, leading a troop when he accidentally stumbled across it and decided to stay, or was asked to stay by Gaspar. Hell, his ultimate form is that of a pink Nu, isn't it? It could just be that once Gaspar learned where he was, that he traveled back and collected one of his Nu friends from Zeal. After all, he is quoted as saying 'All life begins and ends with Nu.' That could very well be where he got the idea from.