Just had the same issue on my Gen 1 , i used Allballs fork kit and couldn't get the top bush to seat all the way same as you, so i ordered gen yam stuff , then a set of forks came up on ebay cheap so i brought them , just changed the oil.
once the bike is together i may attempt redoing the ordinal forks or just sell the lot (forks in bits, gen yam seals & top & bottom bushes)
i have also rebuilt many sets of forks over the years but i did admit defeat on these !!
Mark