I think current Thor would eventually beat DoS DD after a pretty long fight (contrary to popular belief, DD was still quite powerful during that saga.)
You see, without his Mjolnir, i'm not so sure he would beat DoS Doomsday, i'll tell you why. Like you say, almost 20 years later, people have pretty much forgotten the arc, he walked through the JLA, Maxima, etc... He was just to fast for them most of the time and fist to fist Thor is no1t really very much. HE has great endurance, but his combat speed is.. not, even now. I think it would be close though.